Being a far more complicated power plant, there are more Ford Mustang 4.6 problems than earlier Windsor 5.0 problems, but it's still a tough engine if cared for; it just needs more preventative maintenance. There was quite a common problem of failing plastic intake manifolds that can cause coolant leaks on 1996-2001 Mustangs with the Modular V8 engine because the alternator bracket attaches to the plastic manifold and puts additional stress on it until it cracks around this mounting point. If not noticed in time, coolant loss can lead to overheating and engine damage. Unfortunately, there was no Ford Mustang GT intake-manifold recall issued as this is not regarded as a safety problem, so this repair will be for your account. On a 1994-2001 Ford Mustang, P1518 and P1519 OBD-II error codes often accompany intake-manifold problems. From 2002, a manifold with aluminum reinforcement and a strengthened alternator mounting fixed these problems. Check for proof of the work having been done and check for low coolant levels and/or a coolant leak at the intake manifold. That said, there aren't many actual 1994-2001 Fox-body Ford Mustang alternator problems, despite its rickety mounting. Coolant leaks may also originate at the temperature sensor or coolant hose, so check that these are secure.
Spark-plug problems also seem to be a recurring issue on the Modular V8, although relatively few of these seem to plague the DOHC version with four valves per cylinder used in the 4th-gen Mustang SVT Cobras. Spark plugs in the SOHC engine with three valves per cylinder used in other Fords (not this Mustang) can become stuck so tightly that they break when trying to remove them, making the labor bill add up with all the work needed to extricate the broken plug from the cylinder head. The SOHC version with two valves per cylinder used in the gen-4 Mustang may also be afflicted by stuck spark plugs, but it's far less common; however, Ford Mustang ignition-coil problems are quite common and failures may occur prematurely at around 70,000 miles. More than a few owners have reported spark plugs popping out and damaging the comparatively shallow thread in the head, so a thread-repair kit with new thread inserts is quite common online.
The Modular V8 uses a timing chain that is pretty tough, but it can wear out at around 150,000 miles, which is a good mileage to replace it. More problematic than the chain is its tensioner and chain guides, the latter made of plastic in these engines. Never ignore a chain rattle and rather replace the chain, tensioner, and guides in one go. It is critical to use the correct viscosity oil on these engines, as cold-start chain slap caused by a slowly pressurizing hydraulic chain tensioner due to the incorrect oil will wear out the chain guides more quickly. To prolong the service life of these components, stick to the oil changes. On the topic of oil, oil-pressure problems may occur from time to time, so never ignore the oil-pressure light and stop immediately before engine damage can occur. Sometimes, it's just the oil-pressure sending unit, but it can also be the oil pump, so don't take the chance. The Triton 5.4-liter version of the Modular V8 used in the 2000 SVT Cobra R can also suffer oil-pan gasket leaks.
The DOHC 4.6-liter Modular V8 with 320 hp used in the 1999 Mustang SVT Cobra is best avoided. Not only was it recalled for additional intake, exhaust, and ECU work because it was found not to produce the 320 hp advertised, but it was also prone to overheating around cylinders six to eight, causing the valve seats to seat improperly and causing pinking problems. On a Ford Mustang, the P1285 and P1289 error codes usually accompany such an overheating condition, although P1289 may indicate that there's only a problem with the cylinder-head temperature sensor. Take no chances either way. Do not consider a 1999 SVT Cobra without proof that the overheating heads have been replaced and the performance tweaks were done to restore the full 320 hp.
There isn't a lot of data out there on supercharged Terminator engine failures, so this robust iron-block version of the DOHC 4.6 seems tough and lasts well with the proper care. The same basic chain drive is used, though, so the same provisos apply in terms of maintenance to prevent problems.
Mileage: Timing chains can wear out from 150,000 miles, but guides and tensioners can fail sooner. An intake manifold usually makes it past 115,000 miles before cracking but it apparently also depends on driving style and abusive driving can see it fail before 50,000 miles.
Cost: Replacing the timing chain, tensioner, and chain guides will cost around $400 in parts and at least $500 in labor. The updated 2002+ OEM intake manifold costs around $500 but there are some aftermarket options for up to $300. Due to labor requiring up to six hours, this will likely add an additional $400 to the bill - and this may further rise to around $1,200 at a Ford dealership. Replacing the intake manifold with the correct part and replacing blown cylinder-head gaskets due to overheating can collectively add up to over $2,000. A spark-plug thread-repair kit costs around $200-$230.
How to spot: Timing chain problems may show up in a rattling sound, the Check Engine light, rough idling, and P0300 misfire codes when the timing starts to go out. Failed intake manifolds may cause low coolant, visible coolant leaks, overheating, and misfires. Misfires and ignition-coil failures are responsible for most Fox-body Ford Mustang idle problems. Low oil pressure will trigger the oil-pressure light and if ignored, knocking sounds and overheating will follow as the engine fails.