Ok, First off. This i an A model, check the serial number tag above the governor housing. Should have either a DI or PC on here. with a build date of 1988, I would say DI. With out breaking down the arrangement I dont know for sure what pistons are in there. Most off highway engines are set up for torque, not so much horsepower so hard to say right off. And yes this engine does have a timing advance, works centrifigally, similar to a gov flyweight set.
The flywheel housing would have to measured to determine its SAE size. The flywheel should have an internal gear that drives the retarder drive. It will not accept a truck style clutch.
Exhaust studs do break, but if someone puts the manifold back on with out makin sure its flat and the slip joints seized up. and uses a 1/2 in air gun instead of a troque wrench. They will definitly not last for crap.
A 3100 series engine is not bigger nor does it have more power. A 3116 is a 6.6 ltr, a 3126 is a 7.2 ltr. A 3406 is 14.6, do the math. These engines were built up to 425 on highway and 450 off highway.
As far as a transer pump, it should have a gear pump mounted on the drive for the injection pump. This will draw fuel fine. A B model has a different front cover that mounts the air comp higher so the injection pump can be mounted directly to the front cover.
As far a 3046, they are used in larger skid steers and small excavators, under 100hp, not usre why that one was even brought up.