You have a challenge in front of you.
I cannot locate the various posts I saved when the 2000+ engine first started hitting the roads, but there are significant engine control differences in addition the the coil on plug difference you mentioned. For one, the crankshaft position sensors in your new engine have a three pin connector. You could try to install the crank sensors from your old engine.
But, at some point the reluctor gear on the crank was changed and I question if your old crank position sensors will work properly or even fit up to the reluctor gear in the 2000 engine.
And changing the engine type is going to leave you with an incompatible final drive ratio in the transaxle. Not sure it will be a problem, but keep that in mind.
Not to rain on your parade 'cause I would like to see this swap made. You do have other wheels, right? Good luck.