I thought you were on a budget? You are speculating about larger plungers in your nippondenso pump? My guess (I actually don't intend to offend you, but) if you are unfamilar with the differences between IDI and DI pistons and liner protrusion then I am going to take a guess that you may be over your head in changing plungers in an inline pump or retrofiting a mechanical governor Isuzu pump onto a pneumatic governor Toyota engine. My recommendation if you just want a reliable motor and are on a budget of any sort is that you:
1. Remove pan of junkyard motor
2. Remove and replace bearings. Or if you have confidence in your bearing analysis decision making, clean, slather in Lubriplate 105, re-install
3. replace pump diaphragm
4. replace any other suspect gaskets, pilot bearing
5. inspect turbo fins, shaft play
6. re-install motor
Anything beyond this is experimenting and may or may not lead to frustration, stamping of feet and gnashing of teeth. Do not attempt to lower compression ratio, you (I believe) are not trying to build a 100psi compound turbo racing motor.
Gerg is way past all of that and has done all his homework to boot. The reason for compression ratio reduction is simple, He's running compound turbos with more boost than anyone has put on a 3B before.
Everyone is on a budget, old injector pumps aren't expensive.