Lots of people go with the MII setup because they think it's best -- has to be "everybody" uses them! Well, if you HAVE to change the front suspension they are quick and easy -- the SBC of front ends! But they aren't necessarily "better" than the stock independent front suspension (IFS). In many cases they are actually worse! You can't get the range of motion out of the strut rod suspension that you can a real double A-arm setup. Eliminating the strut rod helps tremendously, but make sure you get a crossmember that can take the addes stress! The main reason for the MII swap is just what you were thinking -- easier availability of parts. But if there's an affordable way to upgrade the brakes I'd keep the original suspension. Unless you're going to be road racing it will be as good or better than anything you can weld in with much less time and work invested. This is true on just about any car with ball joints, and AMC/Rambler cars from 1950 with trunnions. If you have king pins or a straight axle and want to improve ride you need to switch to the MII or a derivative.
The mod Ford is wider near the top, but about the same near the bottom as the SBF. You should be able to modify the 55 mounting points to accept the Lincoln mounting pads. I'd keep all the electronics and EFI too. If you have the old Mk 8 available to pull everything from it should be easy. The computer wiring is pretty integrated. Once everything is pulled and dropped into the older car you should be able to connect power and ignition then run. I don't know about the gauges in that year Lincoln -- some years feed off the computer instead of separate sending units for some (or all) gauges. You will have to modify the trans mount, but if you have the Lincoln crossmember that should be easy enough. You can probably modify the Lincoln CM to fit the 55.