thinking about getting a 4.6, are there any issues that i should know about?

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Nope. Just get Full Length subframe connectors. These cars are pretty sturdy if they are maintained well. 96-98 are non pi cars and need pi cams, heads and mannifold to run with the 99-04 cars.

i didnt need h/c/i on my bolt-on nontuned npi car, and would run with and occasionally out run a pi car, but to the OP, these cars love to be maintaned, in return my npi motor went 220k miles. i sold the engine to a friend, hes still running it today. he says its got another10k on it now. the reason i swapped in the pi engine is the cam selections are more vast, along with options for added power. you take care of them theyll last forever, oh my npi motor was beat on quit often. good luck and have fun.
 
sweet! two question, if i get a 98 and do the pi swap (heads, intake) would i be making the same power as the 99-04? second i see alot of cars on craigslist with low mileage with rebuilt motors. thats kinda got me worried.
 
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.
 
sweet! two question, if i get a 98 and do the pi swap (heads, intake) would i be making the same power as the 99-04?

You'd probably make a bit more because PI heads on an NPI shortblock results in a higher compression ratio than on a PI shortblock. The piston dish on NPI cars is smaller than on PI cars...

second i see alot of cars on craigslist with low mileage with rebuilt motors. thats kinda got me worried.

As I said previously, the 4.6 has no inherent design flaws that I'm aware of aside from ****ling **** like a plastic coolant crossover or a shortage of plug threads. Although the pistons are hypereutectic cast and the rods skinny powdered steel parts, the thing is pretty robust. It's not unusual to see a pretty reliable (with a good tune) 400HP at the tires on a stock-internal 2V with a blower.

But these are "muscle cars" and will thus likely have been more abused than other types of cars. People putting nitrous or blowers on their cars can and do hurt them. It's hard to know the history of a used car but one that's had the engine replaced would make me suspicious.
 
Try to find a dealership that has a pair on the lot no matter the years 96-04 and compare acceleration, handling and ride comfort and the quality of the exterior.

Bushings and ride comfort are easy to improve and less expensive. If you are looking for a stockish 4.6 pick the one with the most presentable and cleanest exterior/interior/motor/underbody, IMO. Carfax is a must too.
 
75% of the GT's I see on the road are stock and not being driven by performance enthusiasts, IMO. Because there are so many out there, you can find some really nice ones. Mine had 70,000 on it and was driven by a 52 year old chick. Her 70 yr old husband took meticulous care of it.
 
I would just look for normal wear and tear. The 2v mustang is really a tough car. The drivetrain is solid on these cars in stock form. I wouldn't worry about a high mile car at all, as long as everything else looks good.