-Good first modifications:
Pulley, cold air, Mid-Pipe, axle back, heat exchanger, tune. That should get you to around 550 to the ground on that car. First and second gears will be unusable without drag radials.
-Supposedly those stock clutches go out at around 30k so expect to replace that soon. It might not happen for everyone but it definitely went right at 30k on my buddys car and is a VERY common problem. The RXT is the best clutch for these cars. My buddy used it and so do all the fast shop cars.
-Door panels will begin to peel from heat. There is a really good write-up that details how to scrape and reglue the existing pieces for a factory appearance with better than factory strength. Go that route, don't get covers..
-You may experience an issue where the high speed fan function fails, causing overheating in bad traffic or with AC on. It is caused by a wiring design flaw by Ford and it will typically burn out relays. ALWAYS keep an eye on the engine temp and if it gets high, fix asap. I've read that there is no real fix yet (Except for a replacement harness). Don't let it really worry you but be aware that it can and could happen to yours.
-Steering wheel buttons can flake. Replacements are cheap/easy but it is common.
That's most of what I can think of. Other than those things, the front vinyl stripes overlap on the front bumper and that drives me nuts but oh well. enjoy the ride!