I have been thinking along the same lines. I am thinking of replacing the top on one of mine to create a "mini-MFT". You couldn't use the clamps unless you removed the plastic mess on the other side, but it would work great with the clamping elements.
Below are the answers to your questions.
1 - I haven't removed to top, but it looks to be just a rectangular piece of 1/2" mdf held on by 8 bolts.
2 - I can't tell for certain, but the braces and rail for the top and tool tray share a common rail. You should be able to remove the tray and put a full length MDF top. The tool tray doesn't just pop out. It is held in place with screws from underneath.
3 - Without going out and checking, I think the top is about 1/8" above the molding for the end caps. If I replace the top and remove the tray, I will probably put 3/4" or 1" MDF instead of the 1/2". That would give you additional clearance.
4 - There are only two stops on the legs. One for the scaffold setting, the other extends the legs for the bench setting.
with the leg braces hooked up is far more solid than I thought it would be
When you put the braces on, it is incredibly stable. I have no issues hand-planing on it. The braces are a little awkward, but they work very well.