You don't necessarily book everything in advance, part of the visa application process for Russia, China and Mongolia (I don't know about Vietnam) you will need some sort of Letter of Invitation (LoI). These list things like when / how you will enter country, where you will stay, where you will go, where/when you will leave. These LoIs are not checked once you enter the country, so you can in reality vary your travels as long as you enter and leave the country within dates on visa.
I think from what you say you are not travelling on Trans Siberian, but travelling on Trans Mongolian (Beijing to Moscow via Mongolia)? Doesn't really matter as far as visas though.
Its pretty easy to book trains online for Beijing to Moscow and beyond; agencies like Real Russia are very good but of course charge a high premium.
All in all you will need some idea of dates you are entering and leaving each country before you apply for visas.
As far as Russia a good site from Australia is https://russiau.com/about-me/

Hi! So I can speak to a few of your questions, but not all.
First off, as mentioned 2 weeks is not a lot of time for the route you are considering. Trains and transit options run not as frequently in less dense areas of Russia not along the mainlines, but I can't comment on the exact logistics.

1. What is the most efficient way to link these destinations? I am aware of the sort-of route from Kosh-Agach into Tuva; of the usual bus/train routes between Biysk, Abakan, Kyzyl, and Krasnoyarsk; and of the TSR and BAM routes to the Baikal area. Are there other public/shared transit links that I am missing?

1.Yes, the TSR and BAM lines are where you will find most info on line. There are often buses/minibuses that will venture out of major cities to smaller towns, but as stated the timing of these would be very difficult to hit all the destinations you mentioned and enjoy them in 2 weeks.

More specific questions:
1. If we only had enough time to approach Lake Baikal from Irkutsk, would it be worthwhile? Especially compared to other destinations on the list?

Easily worth it. From Irkutsk take a marshrutka to Listvyanka (the closest and most developed area of baikal near Irkutsk), the ride only takes about an hour or two to get there. Once you're there, there are some really nice hostels where you could meet fellow travels. Baikaler Eco-Hostel is really cool, but it is a long walk up the hill.
There's lots of recreation opportunities by the lake (water activities, hydrofoil, smoked omul, market shopping, nepanarium where you can see the nerpa seals do a show, horse stables, hiking in the forest along the backpackers trail, baikal museum with underwater viewing area, etc.)

1. As far as I can tell, we could be in Kyzyl for Naadym. Should that sway our plans? (again, especially if it means missing out on another destination?)

I've heard naadym is a rough time to travel in Mongolia because of overcrowding and everything booked, but Kyzyl would be less crowded I imagine. If it were me I would try to make it work if I could, because I'm sure it would be an interesting cultural experience. Really depends on what you want.

From this, you shouldn't have any issues as two females, from my experience russia is a very safe place for travelers of all ages, genders, etc.
Not knowing much Russian is the bigger issue. The areas you mentioned stray far from the main tourist areas of the trans-siberian. I can guarantee you the vast majority of tourists you encounter will likely be Russians, if many tourists at all. So don't count on anyone speaking English anywhere. Anywhere outside of Moscow/St. Petersburg and to a lesser extent some university cities like Kazan you will likely encounter very few Russians who speak English.
Couchsurfing is excellent in Russia. Set it up in advance and find hosts that can speak English. They'll likely be a good resource for your ventures and possibly help you along the way. Hostels are also VERY cheap... never paid more than 800 rubs for anywhere I stayed, and typical was like 500-600 rubs.

I can offer some more specific suggestions if you're interested in going to some other places. Ie. Krasnoyarsk is a great jump off point for day-hikes into Stolby National Park, which is highly underrated imo.

All in all props to you for planning this trip! Sounds like you've got some good footing on getting the logistics down.

I expect it to still be beachweather in september, so that is no problem. The water on the Atlantic-side of the Iberian Peninsula is in summer colder than the Mediterranean side and in winter warmer. Adding the Algarve could be an idea, but you'll have to travel by bus from Lagos(?) to Sevilla. https://www.alsa.es/#capa_internacional may be the company that makes this trip. Anyhow there is enough information on this forum about going from the Algarve to Sevilla.
As far as the train-connections between Spain and Portugal is concerned, there are only two: Madrid to Lisbon and Vigo to Porto and both not very frequently.

I'm skeptical than non-commercialized, authentic homestays in yurts exist in China. I think you are far better off looking for such a thing in Mongolia itself.

The only place in Inner Mongolia where I have ever seen authentic yurts (or indeed, actually heard people speaking Mongolian) is in the region around Haila'er, which is a long way from the main "Trans-Siberian" or "Trans-Mongolian" or "Whatever You Want to Call It" route. I'm not aware of any of the authentic yurts up there being open for tourists. There are plenty of commercialized, non-authentic yurts around though, and I suspect local police will try and shuttle you towards those....

It sounds like this is a "dream come true trip for you", and so I really dont want to sound mean or "destroy" your dreams. I totally understand the appeal of traveling overland from Europe to Asia, and stopping on the way to visit the places you have always (for whatever reason) wanted to visit. I did that once and absolutely loved it. But I had 12 months, and still didn't manage to see / visit all the places I would have wanted to visit. I can honestly not see how could do and enjoy such a trip in 6 weeks.

With 2 full days in the cities you mention, yes, you have enough time to see what you absolutely want to see and to get a "tasting" of them. It would be very rushed in most of them, but it would be possible. But its not only about cities, there are also so many beautiful smaller places, and wonderful landscapes and scenery etc. and you with that itinerary you would be totally missing that aspect of the trip. Also, you will need time to travel from place to place. Traveling overland without having the possibility to stop on the way would be a "no go" for me. A good example is Moscow to Beijing - traveling on the Trans Siberian non stop will take you a week. Yes, if you like train journeys its a great journey, but still, a lot of time "only" in a train. I would rather stop in a couple of places on the way.

The easiest route would be through Russia and Mongolia on the trans-Siberian railway. That would get you to Beijing, and then you'd go south through China and cross into Vietnam.

The southern route would go through Iran and India, but it's more complicated because of the war zones and restricted travel areas along the way you have to avoid. Also the border crossing from Bangladesh into Myanmar is reportedly open now, but it takes some arranging in advance to use that border.

A colleague at my office has family in Ukhta and travels there every couple of years. By siberian standards it is a pleasant city, with better incomes than average due to the oil and gas industry, and the climate is not too bad. There is a university, some schools and parks, a giant "Magnit" shopping center etc.
Possibly you can visit the museum about the history of the Gazprom pipeline.
Check out the videos on youtube:
Ukhta presentation: https://www.youtube.com/watch?v=71zAQQP77JE
Gazprom history video: https://www.youtube.com/watch?v=GXG1ArEYkwQ

Hi Michael,

Thanks for trying to help (I think)and I don't know what to say to you either. Different people have different travelling styles and travelling reasons, over my 25 years of independent travel I see my style change through experience, age, or simply mood. I've done fastest route point to point travelling before, of course, thousands of times, and of course also spontaneous aimless travelling, I can't say which I prefer but sometimes it is not up to me.

There is nothing wrong with doing a trip like that. Just like the Trans-Siberian train with 8 days of nothing to do to traverse one country, I actually quite liked it. I got to talk to the locals, mingle with them even without much language, had a great time getting to know them and their culture... and that's a great part of travelling. Even if looking outside the window the scenery didn't change for hours, so what. I'm sure you've heard those famous quotes about travelling not (just) for the destination but also for the journey itself.

I have heard of people traveling by boat to Bolivia from Manaus, even a few blogs about it. I am quite happy to experience it, really. What is to not like about it, you go at a relaxed pace, you get to meet the locals and spend time with them for a few days, you see so many different sections of the Amazon, the life by the banks, and the scenery just rolls by as you watch from your hammock. In comparison to this 5-days trip, 33 hours on the bus is not that long! It's not like you are in a prison bus chained up, you get to move around the bus talking to people, the bus makes rest stops you can go out and explore a bit, and there are windows you can watch the Amazon jungle etc, far more than flying.

I actually already know there are bus companies that does that route, my question was which city (RB or PV) would make a nicer itinerary into Bolivia in the direction of La Paz. There are civilisations along the way, small villages one could visit.. and all of this off the beaten track (hopefully).

There are more options than you described, actually. I'm asking for the advise from especially those who had done this trip or been in this part of the world and can advise objectively. You haven't actually answered any of my questions in my OP, but no offence, what is your purpose for writing replies to my post?