I'm not familiar enough with EFI's to say what needs to be addressed on the fuel management side, I'm sure some of the other guys can chime in for that.
As far as the rest goes, what I would be doing is servicing the lower unit. So I would change the gear oil and I would also change the impeller for sure. After sitting that long, the impeller could very well be dry rotted and who knows what kind of shape it was in to begin with. I would also have a look at the gear oil and see what it looks like. If it's full of water, I would most likely look at re-sealing the lower unit so it doesn't leak further.
What I've always done on powerheads that have been sitting, is I spray penatrating oil into each cylinder and then let it sit for a bit and then I turn the powerhead over by hand (with the spark plugs out so it won't start) and I make sure it's free. I would then change the plugs after it's been run it for a bit assuming the current set aren't in terrible shape.
-Chris