I suspect that increasing the flywheel mass would be necessary to make these engines more gearbox friendly.

Take a look at this thread I started on 4btswaps.com about flywheel weights. The cummins 4BT uses a flywheel with at least twice the rotational inertia of the Isuzu one and it's a diesel of the same capacity.
Heavier flywheel? - Cummins 4BT & Diesel Conversions Forums

My work car is a little nissan 4wd station wagon with a 2.2 diesel. It's flywheel is almost the same weight as the flywheel on my Isuzu 4BD1T. The pictures of Isuzu's 4BG1T industrial engine show a flywheel that is significantly thicker and heavier.
http://www.isuzu.co.jp/world/product...f/b_draw02.pdf