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. In hindsight, I should have ordered a 2 valve dipstick tube but I was worried that the tube length would be different effecting measurable amount. 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. I had already previously installed a X-pipe and wideband 02 sensor, so I had to make a few adjustments to those but everything went together with a little bit a fight.
The rest of the assembly was a breeze and not different than a regular 4.6L until the alternator. The alternator needed to have a custom bracket made to attach to the intake that sat approximately 4 inchs higher (higher deck height plus intake spacers). Temporary ran the alternator without the custom bracket. When the engine was being filled with coolant, I ran into another problem with air pockets. Just like the last issue, the intake sitting 4 inches higher meant the thermostat sat 4 inches higher - higher than the degas bottle. Even using vacuum assisted fill would not get all the air out of the system. The only way it worked for me was to jack the front of the car as high as possible, take the degas bottle off and sit it as high as possible, the vacuum bleed the system. It worked but it was a bit of a pain. In hindsight, the intake spacers had tapped holes in the coolant passages that I would have installed raised tubes allowing for air bleed. I had to cut a large section of the underhood support that would hit the intake plenum.
I do all my own custom tuning using Quarterhorse and TunerPro. Not many adjustments were needed to start the vehicle. I already had a custom tune built for my slightly bigger injectors (Taurus EV6 21lbers instead of the factory EV1 19lb). I did retard the timing a bit for the higher compression ratio. After driving the 5.4L around a bit, I went ahead and purchased a TrickFlow Intake Plenum, 75mm TB, and cold air intake which added a little more air volume, but I think the PI heads and Ford Racing OEM intake are the major restrictions.
While tuning for WOT, I discovered leaning out at about 4500-up. The redline was set at 5800RPM. Turns out the fuel injectors weren't big enough. I purchased some 24lb Ford Racing injectors and tuned them. Now still a little lean on the top end but much closer. My fuel pressure would drop dramatically in WOT. I replaced it with a GT500 pump and now we are all good.