gdmplc66, I am probably one of the least experienced contributors on the board. That said, having completed a ten day, nine night, four city tour, we're glad we had a minimum of two nights in each city. London and Paris alone demand 3 nights or more each (my opinion perhaps) and while we dedicated the most time to Paris (3 nights), it wasn't nearly enough time to cover everything on our list, and that was without the desired and highly recommended (by others) trip to Versailles. But our goals will not have been/be the same as yours.
Initially when I was jotting down everything we wanted to do, I included day trips to various surrounding locations depending on where we were, which if I understand correctly, is what you're thinking of doing? And other than our "set in stone items" -- (connections between cities and a few advance tickets for sights), we decided to play it loose with the itinerary and "try" to keep our expectations in check, and we're so glad we did. For us, the extra locations didn't work out, and that was fine. We saw so much in a relatively short amount of time in each primary city that our trip was full to overflowing. It was a thrilling and busy trip. We didn't run ourselves into the ground, but for the most part we slept very well each night. :)
But, it's your trip and you know your limits, or you will fairly quickly. So plan away. I kind of think the picture will start to clear up once you begin to solidify your plans.
As for the nuts and bolts of planning, we used the resources on Rick's website extensively, along with his guidebooks for each location. For example, he mentions using skyscanner.com for flights within Europe, which we did, and progressed from there. For train schedules we used bahn.de and raileurope.com, also as he suggested.
He has suggestions on accommodations and dining "along the way" as well. The best thing for me, as I was starting from scratch, was to start by reading his Europe Through the Backdoor Guide and then progressing through each city guide. And yes, I read them from cover to cover. Also, his three part travel skills video series, available on youtube, and probably on this site somewhere(?), along with his destination videos, were also incredibly helpful.
All the best to you.