Congratulations on you new girl!
Sounds like you are on a great track with the TnT. I think you're doing the right thing combining the manual valve with the diverters so you don't sacrafice the fine control needed to made precise adjustments.
I was previously unable to post the scan of page 1 of 3 from the Prince catalogue. I've reposted it in this thread so between the three pages you should have all the info you need to generate a part number. Prince has a web site which I think is where I found their phone number, however to buy, I expect they will steer you to a local dealer. I found one in the yellow pages and they turned out to be about a mile from my office. They ordered the cylinders (with a reasonable discount) and had them drop shipped to me.
As for side cylinder length, I don't think I'd change from the 4" stroke if I were doing it again. Unless you have implements where you find it hard to lift them high enough, then I wouldn't worry about it. I did find that you need to cut the side lift link ends off right snug up against the end bracket. The closer you can make the cut, the shorter the resulting side cylinder assembly will be after you weld the end brackets on the cylinder. Another thing I thought about but didn't pursue is drilling another set of holes in the lower bracket above the existing holes. This would effectively shorten the side link and "fix" the lift question/issue. I never checked to see if there was room to do it so it might not be possible.
The top link that I hacked apart I bought from our local tractor dealer. It's an inexpensive imported "generic" top link and I think I paid $10 or so for it, so I had no problem hacking it apart. I'm sure the kubota link is much more expensive and I don't think it offers anything that the cheap link did not. The side link is different - you're paying for the special end brackets and for something that's already welded at the correct angle.
When it comes to welding, I'd take Birds advice about using wet rags to keep the cylinder and rod cool. When I did the side link I think I overheated the cylinder. It all seems to work OK, but the paint on the cylinder started to bubble and that can't be a good sign.
The only other suggestion I'd make is to work out your hose routing to the cylinders BEFORE you weld the brackets on. Specifically, do you want the hoses coming off the top or side of the cylinders or somewhere in between? On mine the hoses come off the top on the top cylinder, and about half way between facing the rear and the right (about the 4 o'clock position looking down on the tractor) for the side link. It all seems to work well and doesn't interfere with my implements.
The only thing I botched up a bit was the placement of the couplers. One of them rubs the seat of my backhoe, and it's also abraded one of the hoses. If I had been able to find a single adapter to go from the valve body to the coupler it would be fine, but I had to use two fitting together so the coupler sticks out farther than it should.
Good luck,
Peter