Yes. I agree that the bus trips to and from Luang Namtha, or too and from Phonosavan are going to take a long time, and not neccisarily comfortable for people with long legs.
Then I want to go to Phongsavan but I suppose I need to stop in Luang Prabang for 1N. Do you?
Yes you need to stop in LP. The bus to Phonosavan the next morning will take around 6? hours.
The best resource for buses around Loas is https://www.hobomaps.com/index.html
It does take a little work to understand how the website works, but if you concentrate, you can use hobomaps to figure out any transport problem in Laos.
I think travel from Phongsavan to Vientian and there take the direct bus to Kong Lor. Seems I can go from Kong Lor to Savanakhek in one day via Thakhaek, no more.
There are buses from Phonosavan to Vientienne that pass through Paksan. You can get off at a place in Paksan and connect with a bus to go through to Thakkek, no actual need to go to Vientienne.
And yes from Konglor caves, you can reach Savannakhet in a day. But depending on your schedule you might need a taxi from Konglor caves to reach a place where there are frequent buses to Thakkek, where you'd get the bus to Savannakhet.