Altima SSS, replacing the intake manifold is certainly no picnic, but definitely doable. And when it's all said and done it feels like you've rubbed your knuckles with a cheese grater.
The way I did it was first pull or disconnect all the ancillary stuff and then pull the starter and drop the collector. You can't get the collector plenum out thru the bottom, but you can move it around enough to make room to get to the lower manifold bolts.
I put it together the opposite way, dropping the collector in unattached, torqued down the manifold and then bolted on the collector.
I'd say, all told, that it took me about 8 hours, give or take.
The TCU is located under the passenger side kick panel, just in front of the door hinge. Tell you the truth, I'm not sure that replacing that had any effect on this, since all these things seem to be inter-related, but I got the part for $20 and it was easy to swap.
After I was done I reset the timing and re-adjusted the TPS and it all fell in line.
BTW, I thinks it's true about the Bosch plugs. I replaced them with NGKs and it seems to make a difference.
Cheers...