If we ignore that what would best suit you is getting a 351 manual truck and swapping it over, I think the best bet is just doing a top end job on the FE.
I totally understand not wanting a certain engine because you don't vibe with it, but what you should consider is time and money vs seat time. I'm at this point with my Capri right now where I am choosing between stroker build or more mild top end rebuild. I would really think about the cost benefit between just throwing trickflow heads and a cam on vs tripling the cost of be build for a third more power. Depending on how you build it, are you going to put the miles on it if it needs premium gas? Will you offroad it if the cam doesn't make vacuum at idle?
I'd avoid the zilla just because it doesn't bolt in like other options will. I don't know much about them, either. Does Ford provide ECU/harness for them too?
You need to ask yourself how many months and years this car can be on jacks. How long are you willing to wait? How much time will you have left to enjoy it after? This post is maybe more introspective than prescriptive so I'm sorry for being a downer. I think its worth considering. That or the Ford psychosis is setting in and I am going to lose it soon.
Ignore what? That I specifically said it'll only be a FE or Godzilla? Not doing a 351 and not buying a donor for anything. Don't need or want to buy a whole vehicle to strip down and dispose of.
Just throwing a heads and cam on it vs the cost of a full build. Did I forget to say that this bottom end is not what I want and very likely has over 300k miles on it? Even if the actual mileage is unknown it is slap worn out and will require a complete rebuild. When dad parked it in 2006 it was doing good to register oil pressure at idle on a real oil pressure gauge. Only reason that it registers decent now is because I installed a high volume oil pump and run 20w-50. Bottom end is getting rebuilt regardless. At minimum it would end up a 390 which requires a full rotating assembly. A 390 rotating assembly costs just as much as going bigger like a 410 or 428, same abount of machine work as well. I'll run what ever fuel the engine build requires. Premium gas is no worse per gallon than the diesel I've been putting in the F-250.
What about restomodding the truck makes you think it will be an offoader? Yes, I'm going to install a 4" lift kit, but it's always had a 3" body lift and looks right that way. I'm just swapping BL for SL. Yes, it'll be driven on dirt roads, but not offroading the likes of what you guys run. I've got an ATV for that type of stuff. Also if I don't get parts for lowering it more soon (or I'm not happy with the results), the '99 Ranger V8 swap may end up with a 4wd transfer case, lift kit and 33s. If I wanted to come play off road, it would be the toy of choice.
With the exception of an inline 6, no other options just bolt in. Any other engine is going to require custom mounts, those were the only factory engine options in these trucks. For a SBF I'd have to track down a pair of late 70s frame towers, or spend on custom engine mounts. For the Zilla or anything else I'd have to do custom engine mounts. Fortunately companies sell conversion mount kits with the engine side already done, so it's just a matter of positioning the tngine and using the supplied bits to finish out the frame side. I may have even found a bolt in engine mount set for the Zilla, just have to verify that it fits the 67-72 F-100 4x4 since it is sold for the 73-79 F-100 4x4. I think that the main frame differences were wheelbase length and different shock mounting.
Ford sells the Godzilla as a crate motor. They also sell control packs (aka the EFI system) designed for running a Godzilla as standalone. Just a few wires to hook up and make it run. Probably even easier than wiring up a 5.0 swap in a Ranger. There are also a few companies, including Holley, that make aftermarket ECUs that can run them.
As the truck sits with it's work out drivetrain I can't really enjoy it anyway. It can be on jacks as long as it needs to be, but I don't see it taking more than a year, maybe two. It'll largely depend on how much trouble I have waiting with body work end of things. Disassembly and assembly won't be difficult, just got to work around the weather. Having a shop to work in will help things along greatly, but not having AC will make a few months of the year prety rough to work in. Not that it matters, I wasn't driving the truck during those months anyway due in large part to no A/C the truck. That's going to change during the course of the build.
Having just turned 40 and a grandmother that is about to turn 92 and still going strong, hopefully over half my life left to enjoy it when I get done. Dad got taken at 71, but he also had a few very hard knocks that seriously drug him down. Starting with a plane crash that caused mobility issues, further mobility issues stemming from those, developing a sedentary lifestyle as a result, stroke, cancer, more strokes, all things that built upon one another. I honestly feel that if he hadn't been in that crash, he'd have stayed a lot fitter and would likely rival his mother in lifespan. Besides, if I worried about how much time I'll have left, I'd never do anything.