The plan is to upgrade to the turbo. This places a strain on every other part as every other part is designed to make only 98 HP. So finding the weakest link is easy. Which part when changed gives more power?
The reason that I found it was I placed the turbo on it and checked back in the engine area and found that both sport and race turbo only had a gain of 7HP. I put on the intercooler and it went up to 14 on the sport and 10 for the race. (scratches head) Exhaust did the same thing.
I've seen intakes jump a couple because of a filter upgrade and I've also seen them drop one because of too good of a filter upgrade weakened the air charge.
As a preliminary guide, go filter, ignition, carb/fuel, intake. That's how to work the front side in order to reduce restrictions and increase efficiency. Most rear sides (exhaust) are as big as you can. Plus they just sound cooler.
I would save the displacement until the intake side has been addressed. Should be a big pick up there. And really worthy for the rev happy VTEC crowd. In fact you might start there and compression with those as they have a gain across the board.
It will also be interesting about the flywheel upgrade. I would think that too much would hurt a small, high winding engine. Might be worth to check out. I would say start/finish on the 'Ring might have enough grade to prove it. Too light of a flywheel on a small engine actually loses hill pulling power. With a cylinder firing each 180 degrees of crank rotation (in an I-4) the flywheel stores it and smooths out the power output. V-8's have one fire every 90 deg.