anyone used 3 valve pistions in a 2 valve motor?

I would suggest calling Manley and working with them to identify the correct pistons for your application. They probably have a customer service number.

Ehhhh, dont think thats a good idea. Is 2 of the valves even in the same positions as the 3valve engine? Meaning the valve cut outs might not even line up if you were to put it in a 2v motor.

That just doesn't seem like a good idea. Why not just get the CORRECT high compression pistons

You can use any 90.2 mm piston with standard compression height in a 2V. The 3V valve reliefs do not come into play with the 2V. The closest point the valve comes to the piston is along the upper surface of the ring land...that 10 mm radial flat area on the deck of the piston. No matter what size dish, that flat is constant.
The 3V's have valve reliefs that interrupt this flat area, but in a 2V, they don't give you any additional clearance. (No, the 3V intake valves are not in the same location as the 2V valves, relative to bore.)

All of the modular v8 pistons have offset pins. They just vary from ~.8 mm to ~1.3 mm. It's to alleviate piston slap. Your 3V 4.6L is a .8 mm offset and the 2001 2V 4.6L for example is 1.3 mm.
This offset makes it imperitive that you install your pistons in the correct orientation. There are "front of engine" indicators on these pistons. If you get them backward, you're gonna have problems.

I'm going to be insalling a 3V short block this winter. I'll let ya know how it turns out.

For the '99 Lightning, the offset is 1.27 mm (1.15-1.39).

Your gasket thickness should be .038" itself if you're using a stock thickness. Add in the piston to deck clearance. I don't have that dimension, but I believe it's more than the .0118" of the 4.6L. Someone will chime in with that.

'99 standard 5.4L offset should be 0.5 mm. That's the only dimension I could come up with for a '99 truck application. Without the actual part number, I can't guarantee that dimension.