Once I had everything prepped and the heads put together, it was time to assemble the engine on the stand. I wanted to buy a set of ARP Head Studs but it wasn't really in my budget for this project. Instead I bought the 3 Valve Ford Performance Head changing kit. Before you ask, yes it will work in my situation. I put the heads in, put the camshafts in, and then set up the timing chains. Nothing different than the usual. I purchased a 3 valve timing chain set to use with my 2 valve heads and it worked flawlessly like my previous mock ups with the worn out junk 5.4L that I used as a core. After setting the chains, I pre-lubed all the lobes and roller rockers and installed them all.
A hugely important part of this swap is the use of the adapters plates. I originally installed these plates with the supplied gasket on the bottom of the plate mated to the cylinder head. That created a problem later when installing the ford intake gaskets on top of the plates. I ended up removing the paper gaskets and buying another set of Ford intake gaskets. *More problems encountered and described later*.
When I go to reinstall all of the spark plugs, some serious bad luck happens. One of the spark plugs would not get tight and just ripped the threads right out of the head. Luckily, I knew how to repair blown out plugs on 2 valve engines. A slight delay, but fixed right up.
A small problem I ran into was that I ordered a 3 valve 5.4L dipstick and tube. The 3 valve is set up differently and the bolt doesn't line up with the hole and the tube doesn't fit well through the exhaust manifolds. I got it to fit OK with some finesse. I also decided not to mess with EGR so I plugged up the tube coming off the manifold and cut the tube off the EGR valve so that I could temporary still mount the valve to the intake plenum to stop the vacuum leak.
Aside from this, I pushed forward: time to set the engine into the car. It was such a tight fit that I removed the transmission to make my life easier. It still was a bare to get in. There is hardly no room on the sides, no room between the AC lines and brake booster accumulator. I forced it in by tilting the engine and using a pry bar to help guide the motor mount studs into the hole.