To gain a significant advantage in resolving the problem you are having, the afm's have to be after the intercooler, as the air still bounces in the hot pipes. YOu will almost certainly have to make metal housings for the afm's if you want to run serious boost, as the housings crack. IMHO doing a plumback setup will be far less work and less likely to get you a defect..
Is the wastegate flap cover passages for both sides of the housing. You may want to look at upgrading to an rb25 manifold, as they are a little bit better than the rb20 ones if my memory serves me correctly.
Rb 30e wont come close to clearing the bonnet, as the sohc head is heaps taller than the dohc head. I also doubt you could get it engineered, as the rb30e is a 86-87 motor, what year is the cefiro?
Dont see how silicon joiners will help you with the drivers side, unless you buy a longer silicon elbow to replace the rubber pipe that goes to the plenum
Your 044 shouldnt outflow your stock lift pump, as there is no pressure working against the lift pump, if it does, the problem will be worst at idle, as the 044 will flow the most then, due to the low fuel pressure at idle, so it shouldnt be dangerous to test.
There is absolutely no need to upgrade rods at that power level. You could upgrade pistons, especially if the bores are a bit worn. I would pull the crank out and have it linished with a crank collar fitted. There is no point fitting a new pump without a collar. You could fit an aftermarket balancer to improve the life of the pump. If it doesn't see excessive revs/rev limiter then the n1 pump with a collar should last fine.
OIl restritors are about the only thing i would add apart from the new bearings of course.