I think you can pick up a mtx 75 in all foci up to 2011, its the standard 5-speed option.
the only other transmissions available was the automatic, and the getrag 6-speed for the SVT.
there are 4 engines available that year here they are in order of worst to best.
The Zetec is a very solid and reliable engine, you cant go wrong with it. The SVT is basically just a pepped up version of it. The Duratec 2.3 is harder to find, but its the torquiest of the bunch, and arguably the best engine available.
Just avoid the SPI. (which were only available in the wagon and sedan format, get a zx3 or zx5 and you are ballin)
Regarding electrical issues, i've never seen anything major besides the occasional alternator, or 02 sensor. I will say though, that the 2000s and 2001s had more problems than other years, ford mostly fixed the problems by 2002+