1) You don't need to go to Doradal to continue towards Medellin. The reserve has a big arc-like entrance and entrance sign and is at a bend in the road. This is where you'll be dropped off and can catch a bus. From Bogota you're basically going to catch a Medellin bound bus.
From the entrance it is a 20-30 minute. It's not hard... hmmm the wheels will definately get dirty, it's a mix of gravel, dirt I think. I'm sure you could suck it up, it's not ideal but I think renting a car and driving is such a pain... depends how comfortable you feel.
Not sure your experience with buses in Colombia, but flagging them down is common as is requesting unusual stops in the middle of wherever. Both those are pretty standard practice. It's worth re-reminding the money collector guy depending on how sharp he seems, or just sit up near the front where you can be a constant reminder.
Also worth mentioning as I think you might have this detail off - but from Rio Claro you don't need to go all the way to Medellin. You will be looking for a Medellin bound bus, but tell them you're going to Guatape - you will be dropped off at the turn off to Guatape, this saves a few hours in bus backtracking. Being dropped off you'll now feel like a hitchhiker on the side of the road cause there doesn't really seem to be a great spot for a Guatape bus to stop, but if you flag it, it'll stop.
Also you'd asked about cutting out Guatape for more Jardin time... I would give a reverse variation of that idea - if you are loving Rio Claro and want more time, cut Guatape. And not to suggest you should just I would take that approach. Cause it's easier to decide you should cut something cause you're certain you love the current spot then imaging you might like Jardin more. You won't really know. I liked Rio Claro and Jardin more. Guatape is more of a weekend getaway town, I spent a Sunday and Monday and found it pretty quiet on the Monday, actually enjoyed the Sunday with all the crowds more. I'm glad I went, just I would pick the other 2 if I only picked 2.
I think any of the car rental stuff or traveling with that style of suitcase I don't have enough experience with. But the walk into Rio Claro isn't crazy up and down, not perfectly flat but it's not like doing a hike in the Rockies or anything... almost wondering if there could be a moto-taxi option or not. I took one from Doradal, but can't remember if any of those guys were actually hanging around the RC entrance.
I did Rio Claro, 3 nights (cause we went to Hacienda Napoles which ate up a day), Guatape 2 nights, Jardin 2 nights. But there's no right or wrong answer, your plan sounds fine. I suppose if you loved Rio Claro you could also look at like skipping Guatape saves some logistical hassle too, you'd just go straight to Medellin.
Leaving from Guatape to Medellin is easy, there's a small bus terminal so you can check times, I think it was hourly or something though. Let me know if you can any other questions.