A few things worried me about using 2 valve heads on this brand new 3 valve block. The first of which is simple, the oil pump. A 3 valve oil pump is extremely high output otherwise comparatively speaking. I decided to trade out the new 3 valve pump and install the 4 valve Cobra pump. That pump also has a guard build into it to help prevent slinging the oil up the chain.
Reading on casting spec changes on the 3 valve blocks, they raised the head bolt threads inside of the block so that the thicker 3 valve head could still use the same head bolts. It looks as if they raised the floor of the head bolts as well, but it did clear when torqued with the 2 valve heads on it. Everything else lines up as normal.
Clearly the 5.4L oil pan was not going to fit my New Edge stock K member, but since I had a 3 valve 4.6L oil pan around I'd figure I would give it a go. Not quite sure on the fitment yet, but it is bolted up to the engine on the stand. Based on loose measurements, it looks like it will barely fit. It holds a quart more. The motor mounts are in the same locations.
Swapping to the 3 valve 4.6L oil pan created an issue of it's own. On the WAP 4.6L blocks, Ford installed a windage tray that bolts to studded mains. 2 valve 4.6L and 3 valve 5.4L have baffles in the pan instead. Even if I purchased studded mains, I do not believe the 4.6L 3 valve tray would fit. I ended up purchasing a GT500 oil pan gasket/windage tray combo. It had to be slightly modified to fit the 3 valve pickup tube, I drilled a few extra holes for drainage since the head oil drain holes don't line up. A little more trimming off the front was needed to get it to sit down. At the time, I wasn't sure the pan would fit the stock K-member but it did without issue. The sway bar is pretty close to the drain plug so changing oil isn't as easy anymore, but the pan does hold an extra quart of oil.
With the heads off, I purchased some reground stock MHS intake valves (previously purchased when planning on the 4.6L build), so I pulled the cylinder heads apart and cleaned them up. I took part in a home remedy port and polish job. I should rephrase that a bit. I cleaned up some casting marks, slightly port matched, lightly polished the intake side, and cleaned up the bowl area. I figured screw it and gave the guides a slight taper. Then I lapped in the new intake and old exhaust valves and replaced the valve seals.
Since the engine has a 8 bolt crankshaft, I ordered a new Exedy stage 2 clutch as well as a Fidanza Iron Nodular Flywheel. A few other misc stuff was ordered as well. Exhaust manifold studs and nuts, head gasket set, that sort of thing.