One piece of advice I would give anyone - stay away from big block A-bodies. Everything's more complicated than it should be because the fit is so congested.
I'd qualify that statement a bit:
"Stay away from big-block A-bodies
unless it's 100% original or you're going to build it yourself from the ground up."
You had the unfortunate circumstance of buying someone else's project, not knowing any of the half-assery involved when you did so. You knew it had elephant ears but not that the engine location wasn't given much thought (beyond maybe header clearance?). The engine wiring harness was likely butchered to do it, but that's not the kind of thing that jumps to mind immediately when buying a car (especially if it ran). The true condition/build level of your engine and transmission are still question marks. You sauntered into the half-done project of a mentally-unstable individual.
On the other hand, had you bought a Duster with an empty engine bay or an engine you planned to remove forthwith, I'd wager half the problems thus far might not have occurred. Knowing exactly what you have initially makes an enormous difference: "I've got a 318 car into which this here 400 is going. The wiring isn't going to work as-is. I'm going to need either swap mounts or a factory B/RB K-member. There are only a couple of header manufacturers that won't require cutting the inner fenders but that's going to require a later-model or custom starter. The driveshaft is going to be wrong." You're aware of what needs to be done, rather than stabbing at or discovering what needs to be
redone. And that, my friend, makes all the difference in the world. You'd probably have been better off in the long run ripping the engine/trans, elephant ears, and engine wiring out of the car and keeping only the former. "Now, how do I correctly make this engine fit and function?"
Though the confines aren't quite the same, putting a W2 engine and 4-speed into a slant six automatic car had its own considerations. The OE engine harness is now a connector donor; I went ahead and sprang for a repro 1969 340 engine harness (using a 30% off sale code, of course). I used known-workable V8 adapter mounts, despite knowing the location of several V8 K-members I could've used. I knew I didn't want the breakage-prone 1960-'72 transmission mount on a 4-speed behind a high-powered V8. The driveshaft wasn't going to work but upgrading that was a given at the outset.
The point is,
I had a list. I
knew what had to be done. The two biggest tribulations I had were in trying to be frugal by using 1/2"-thick adapters to convert the W2 exhaust port to a standard LA header (absolutely not happening in an A-body) and finding a '73-up trans crossmember. I wasted several days of my life on making, then trying to get those exhaust-port adapters to fit. That was a problem I created by avoiding a known-good configuration (the TTi headers). The trans crossmember was a bolt-in once I found one. The conversion motor mounts required a 3/16" spacer between the LH insulator and the mount to lift the TTi header off the steering box--easy fix, but that was the only real compatibility issue I had to discover. Any other problems I encountered were generally of my own creation: using the scattershield, installing a clutch switch the car would've never even originaly
had (clutch switches didn't exist pre-'70) etc.
I'll say this: that Year One engine harness was a godsend. All the right wires in all the right places, and
all known good--not 50+ years old. I modified one wire in order to use a '70-up voltage regulator. Everything else was perfect, leaving me lots of time to create my own issues.
While I realize there's no B/RB '71 Duster, the engine harness for a '71 Duster 340 with electronic ignition (it was available in '71) would only require lengthening the coil and distributor wiring. You don't even have to cut the distributor harness; just lengthen a Hopkins part #47965 or recycle two pigtails from distributors/harnesses). "I know there are no wiring issues between the firewall and core support" is an enormously-good feeling, trust me.
The big-block A-body swap was not only a factory option, it's something that has been replicated literally thousands of times with good results. It's a great swap when you know exactly what lies ahead, including the expense. In your case, half of the issue has been what lay
behind, i.e. "exactly what did this hammerhead do?" or "what was he thinking?" It seems most of your time on this project has been chasing down those questions and issues. Those are the least-fun problems to have.
Perhaps a better warning would be "
Avoid someone else's half-baked, half-finished bullshit project no matter how appealing the final product might be."