Hi Huttler, welcome to the Blue Oval side
Just FYI, the 94-95 cars use the good old pushrod 5.0, and are very easy and relatively cheap to mod...
96 and on:
In my opinion, the late-model modular motors are very stout, reliable, engines.
The only major issue I know about is the stock "plastic" intakes on the early 96-98 4.6 GTs. They like to grenade themselves (crack heavily) whenever they feel like it. Most of the time, it will fail after some boost has been added to the set-up. Mine grenaded shortly after the install of my Procharger P1SC blower. But I have heard of many occasions when one has grenaded through normal driving.
There is currently a TSB out on this and Ford will replace it for free on the 96-97 models if it fails "under normal use". (in other words, don't drive in there with a blower or a nitrous kit strapped on)
Also notice that I didn't include the 98, which is not in the TSB but seems to be the exact same intake....
The issue does not exist on any 99 and up Mustang...
I've also heard some grumblings about the early (96-98) T-45 transmissions letting go, but this too has (in the most part) been rectified by Ford in the 99 and up models.... and some may just miss the T-5
As far as reliability:
I bought my car brand new in late 97, and other than the intake issue, I have had no problems at all with stock portions of the car.
I do have an electrical problem while using my custom Auto-Logic chip, but I can't blame it on Ford...
I'm currently running 450hp at the flywheel with drag radials, go to the track often, and I'm still running great on my supposedly iffy early T-45. The stock clutch is just now giving me just a hint of trouble at 50,000 hard-driven miles. (It's time for a King Cobra clutch) I've only had to do some regular brake service (pads and the like) once. And guess what else? Not one squeak... Rides as quiet as the day I bought it...
While I absolutely HATE dealing with Ford service departments, the car itself has been worth every penny of the original 20k I spent on it.
Hope this helps...