thinking about getting a 4.6, are there any issues that i should know about? Like too much body flex, runing hot or ????
Can you be more specific? Year and model of interest?
These cars are closely related to the Carter-era Fox Mustang so don't expect drum-tight chassis, especially on the convertibles. This can be mitigated some by SFCs as mentioned above though not much can be done to stiffen the 'verts as they already come with additional bracing (including SFCs) from the factory and still come out being pretty flexible.
If you're in the north I'd steer away from any Mustang that's seen winter duty and salty roads. Any car is going to have a tough time in those conditions. I'd only consider such a car if it's been oiled yearly and passes a close-up visual inspection.
Mechanically, they're simple and pretty reliable. The 4.6 itself is a rock, used in taxi and government fleets. Early cars had issues with a plastic coolant crossover in the intake manifold cracking. Later cars had a revised manifold that addressed that though. Some cars have shown a tendency to eject spark plugs due to a design where few threads were provided in the head. If this happens, it can usually be fixed with an insert without removing the head. Just check the plugs periodically and listen carefully for sounds like exhaust leaks from under the hood...
The transmissions are pretty solid. The Tremec TR3650 used in 02-04 cars was noted for having grinding issues on the 1-2 shift when cold but Ford issued a TSB for a repair. It'd be surprising if there were many cars out there that hadn't been fixed. The rear axle is tough and durable. The
suspension is basic but tough and basically trouble-free. On later Cobras an IRS was used that's subject to wheelhop, easily fixed with bushing kits.
If you're looking at a used GT Mustang you're probably going to be looking at a car that's seen a tougher life than most cars. Comes with the territory. Make sure you carefully inspect whatever car(s) interest you for signs of abuse or neglect.
My Mustang is one of the most reliable cars I've ever owned despite a mod or two here. Then again, I meticulously maintain it and don't truly abuse it.