Okay, so I ditched the Novi route. I decided I want to do a 5.4 2V swap instead. I priced a 5.4 from a F150 with 96k miles at the local Pick-n-Pull, going to run about $550 for everything needed from the donor truck. A local chop with do a total rebuild for $600. So in total that's a little over 1k for the shortblock. I know I will need a HPS Intake and PI heads. I am looking at picking up a set of Stage I PI heads from MMR to compliment the intake and shortblock. The questions I have are: Could I run a set of BBK shortys without clearance issues? I picked up a set on CL in mint condition for $70 and I really would like to use them if I can. Also, if I used the adapter plates, could I run a 2.1 KB on top of the 5.4? What about a P1SC? Would I have to fab one from a 4.6 kit or could I just used the whole kit with no fab? How much power can a 2V 5.4 handle? Reps given for responses.
What are your goals for the vehicle and what is your total budget? If you are looking primarily for track performance, you won't see a lot of improvement with the 5.4; especially considering that you are looking to go FI. The limiting factor with these motors is the heads - which are shared with the 4.6.
If you are looking for a broad torque band in a streetable N/A package (which is why I am building a 5.4), then the longer stroke begins to make sense. Not that the 5.4 can't be a track performer - it just takes more work to put together a good combination.
For the headers: FRPP and JBA shorties are known to work. The BBKs may work, if they are the unequal length variety. The equal length versions will likely have clearance issues - you won't know until you try.
For the shortblock: The 5.4 rods are no stronger than their 4.6 counterparts. You will want to invest in at least an inexpensive set of H-beams, if you plan on spending any time over 5500 RPM. Figure another $300-400 for rods and a little more for balancing. You can check if the crank is cast or forged by visual inspection. Knife-thin casting lines indicate a cast unit; thick, flattened seams indicate a forged piece. Cast should be okay if you stay under 6000 RPM and don't run big boost. If it were me, I would invest in a set of pistons while the motor is apart - you can pick a compression ratio to match your application and pick up a little strength.
Intake: The HPS is a good choice (well, the only choice) for a streetable N/A application, unless you want to spend a couple of grand for a custom sheetmetal unit, then more for fabrication work and a big cowl hood. Adapter plates will kill your mileage in a street-driven car, due to offset injector placement, relative to the intake valve. For F/I applications, Tork-Tech makes a three-piece blower manifold that can be widened with vertical plates that don't affect injector placement. A centri blower kit should work with the HPS intake, but some minor fabrication (e.g. relocating bolt holes, etc) will likely be needed. IMHO, if you are going FI anyway, you will be better off with a 4.6, as aftermarket support is much better for the shorter block.
Heads: If you are going N/A, you will want stage 2 or aftermarket heads - stock and mildly ported heads will run short of breath very quickly above 4700 or so RPM. You can run longer duration cams in the 5.4 than in the 4.6, unless you get zero-decked pistons. The longer stroke and increased volume will tame the cams a bit, so in general, driveability with a given cam in the 5.4 will be similar to driveability with the next size smaller cam in the 4.6.
Tuning: If you are F/I, you will want to get a dyno tune right away to avoid trashing your investment. For an N/A build, you can probably get away with a mail-order tune for awhile. A mild N/A build will run on the factory 4.6 tune, though probably a little rich judging from the feedback I have seen (and judging by my current mild stroker setup). You will want to bump your injector sizes up for all but the mildest N/A builds (tune required).
Most of this info was gleaned from this and other forums. I hope to have first-hand info by spring or summer (got heads, block, cams and crank; waiting for rods, pistons, intake and headers). I have a 4.6 stroker now, and I can tell you that the longer stroke does make a big seat-of-the-pants difference on the street, as there is much more torque available off-idle.