I think the clue here is the "after years of it being in pieces".
I'm not sure it's possible to fit the flywheel 180 degrees out, as the slot is offset to one side. As Sprocket says, using the wrong clutch (diaphragm) will put the timing out, but it looks like you've fitted the original, so I'd look elsewhere personally. I've not done mine for a while, but I'm sure there's pegs on the diaphragm to flywheel bolting points to ensure it's the right way round (?)
I did a rebuild (SPi) that took about 3 months (over a hot summer) & the injector refused to open even after that short time, so the dry plugs would make me look in that direction.
I did get the old one to work again, but it took a lot of new fuel & Redex before I got a clean spray pattern.
The Crank sensor dictates spark and injector timings, so if you've got a spark, then you're obviously getting a signal, so no reason to panic yet....
Have you tried cranking the engine whist squirting Easy Start into the filter housing? That would be my next step.
I did manage to get the injector squirting by removing the plug & connecting 12v between the points - obviously the system needs to be pressurised & you need to pulse the signal. This was easy to see on the SPi, but not sure if that's possible on the MPi.
Can you check the injectors on your ACR? Mine has a function for this, but again only used it on an SPi.
I'm sorry I can't help more than that, but I really don't stink it's the flywheel - unless you changed the clutch / diaphragm.
Good luck
MA