new engine

Hi, I have a 97 mustang GT with 124,000 miles, with all kinds of mods done to it. The previous owner did all the work to it, and while he wont admit it, I suspect he raced it pretty hard. The mods include 155 LPH in-tank fuel pump, BBKfuel pressure regulator, BBK fuel pressure guage, upgraded motocraft 8.5mm spark plugs and wires, BBK cold air intake, K&N conical in fender air filter, BBK ceramic coated full length headers, BBK 2 1/2" off-road H-pipe, flowmaster 2 chamber mufflers with sayin tips. SUSPENSION-maximum motorsports 4 bolt caster/camber plates, maximum motorsports front coil-over kit, KYB AGX adjustable struts, hypercoil springs(front&rear), maximum motorsports rear coil-over kit, koni dual adjustable shocks(yellows), edlebrock dual adjustable upper control arms(pinion angle adjustment). EXTERIOR-billet grille(with pony), 95 cobra R rear spoiler, 99-04 GT fender emblems, 18" chrome bullitt wheels with 275/40/18 nitto 555 extreme tires. INTERIOR-suede racing seats, 03-04 cobra pedals, B&M pro-ripper short throw shifter, 02 cobra center console with leather e-brake handle. DRIVE LINE-drive shaft safety loop, 3.73 rear end gears, centerforce dual friction clutch.

My problem is that 2 weeks ago the engine started doing this "loping" action, when ever I floored it, but would stop after it got to 4k rpms. Just yesterday it started making a real loud ticking/clanking noise, at first I thought something was touching the fan, but it sounded like it was coming from inside the engine. We took it to get looked at earlier today, and the shop said it sounded like I would have to replace the engine. They said even if they could fix the problem, a car like this is going to start having more and more problems, because of the way it has been driven. Well since it looks like I'm gonna have to get a new engine anyways, I was wanting to get a 99-04 4.6l, and was wondering if this would work. someone told me the computer might not be compatiable, or possilby the transmission would not work. Any input would be greatly appreciated.
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svttech76 said:
the 99-04 engine is a drop in.

the only thing is making a t-fitting for the extra coolant sensor you have in your NPI car. thsi is a very easy straight forward swap.

+1 The computer will work with a new tune, and the transmission will bolt right up. As far as a cobra swap, people have done it, but $$$$$.
If your going with the 99' + engine you'll need to use your existing fuel rails and electrical [coil paks, sensors, alt] If the new engine has an aluminum intake crossover, it's best to have it tapped for the extra sensor, if not, then you may have to use the T-fitting if you can't find a spot on the side of the block to mount it. If your current non-pi engine has had the intake replaced, it may already have the aluminum crossover, in which case you can use it on the new engine.