Ford Modular engines can easily be swapped back and forth using the same generation of engine, but you can actually swap parts between those generations as well to create different higher performing combinations. For all those Mustang and F150 swap guys looking to make a few extra ponies, listen up. Lots of this information was gathered from online forums and other sources and compiled here mostly because of my own research for my engine swap in Tech Tales.
Pre-1999 4.6L 2valves were NPI. Featured a 11cc dish piston and 51cc heads (9 to 1). A swap to 99+ PI 42cc heads would put you around 10.5 to 1 compression ratio and pickup 40hp over NPI design.
1999-2004 4.6L 2 valves were PI. Featured 17cc dish pistons and 42cc heads (9 to 1). A swap to a pre-1999 block would put you around 10.5 to 1 compression ratio and pickup 5-10hp. Easily a junkyard performance special if you need an engine anyway, otherwise not worth the effort..
2005-2010 4.6L 3 valves block. Feature a 7cc dish piston an 49cc heads (9.8 to 1). Aluminum block. Using this short block with PI 2 valve heads will net you a high 11.5 to 1 compression ratio while saving weight (around 80lbs).
2004-2010 5.4L 3 valves block. Feature a flat top piston and 49cc heads (9.8 to 1). Using this block with PI 2 valve heads will net you a 11 to 1 compression ratio. Also has piston to deck clearance of .120 inches so it has more valve to piston clearance for radical cam choices than the 4.6l.
4.6L 2 valves oil pans have built in windage tray as do 5.4L 2 valve and 3 valve pans. The 4.6L 3 valve pan has a windage tray that bolts onto the main studs. If you are swapping things around, I suggest ordering the GT500 oil pan and windage tray. It will require modification to fit but is a much more sophisticated piece than the Canton.
Using a 4v block from a 1993-1997 Mark VIII or 97-2004 Cobra with 2V heads would also bump compression way up into 12.5 or 13 to 1. A good combination would be this block with a set of trickflow 2v heads running on E85.