GottaBigBlock
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What year mustang did you put the PI heads on? If it was a 96-98 GT, then yeah it would make a difference because they are better designed for flow and would increase the compression a little more than the heads they replaced. I doubt it would be worth swapping 4.6 heads onto a 5.4 though. A 5.4 swap seems like you have to fabricate headers no matter what unless you have measured to see if the stock manifolds will even work. I would just swap the 5.4 3V in and get it running before you worry about adding any performance mods to it.
they went on a 2002 Ex 4.6. The originals were damaged in an engine incident(I'm still not sure what happened to this kid's Ex but it bent valves, dinged up the cumbustion chambers and one was absulotely un useable, so his dad got those heads( They came fully dressed and ready to install.) and I put them on for him. (note: the install kit is pretty comprehensive, I would recommend buying the kit for anyone doing this head swap)
Also, the stock manifolds will fit but will require a pretty serious offset downpipe to get it to clear the framerails. This would definitely have to be fabricated and welded because the complex bends won't let it be bent on a mandrel or tubing bender.
the only other clearance issue I'm concerned with is the driver side head to the master cylinder. looks like it will be OK but a little tight.