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No, with the other changes made you would need to do more then swap-in the heads.
You would be better off trying to get an '02 complete engine and do the swap.
They made some changes to the cam profile as well as the PCM program. This has been looked at before and you would better off trying to swap in a complete motor & assoc. parts.
I can't remember the year they changed the HP&TQ ratings. As long as your truck falls within that change you should be okay to swap heads. Any early 99 or 99.5 cannot be have the heads swapped. You can look at the motor and there will be a PI (performance inhanced) casted in the heads/block on the higher HP motors.
The parts may be the same in all V10s but the PCM and cams may make the difference. You would need to check part numbers between the years to find what is different between the motors.
Have a '99 V10, want to know if I can put a set of
heads for an '02 or newer on it without any problems ?
There are a few Mustang V-10 sites that are around. There's also some shops specializing in this swap. I would think they would be the one's to ask about this swap. There are guys doing V-10 cams, and there is no accessory manifolds being made but there is work you can done on your manifold. I would definitely look around at some sites and see what's the hot set-up prior to buying newer stock heads. A supercharger will add alot more hp than adding newer heads, for probably close to the same price. Adding headers, a new throttle body and a chip will also take you over the newer motors hp ratings for alot less $$$.
I think that it's basically the same as doing a PI swap on the 4.6 Mustangs. The heads, cams, manifold, and PCM must all be swapped. The actual combustion chamber on PI heads is is much smaller. The PI heads also flow better than the standard ones. I'm not sure, but I believe the intake port shape might also be different on PI heads as well.
Muscle Mustangs & Fast Fords did a 4.6 PI vs non PI story. With a little work the non-PI heads out flowed the PI heads. So the same should be true for the V10. But like someone else said just go with a SC or other up grades. I don't like to dig into a motor unless there is something wrong with it. My 2 cents on the subject.