Have D2 3J 4346 that I purchased not running but "was running when parked".  Got diesel freed up, and pony runs.  Fan turns when I engage the diesel, but pony gets pretty warm fast and no heat in diesel.  From my understanding the 3J's don't have a coolant bleed at the pony like the 5U?  Doesn't seem like the water pump is moving any coolant.  Any tips, or just pull the pump and check on it?  I would have expected some semblance of coolant disturbance in the top of the radiator.  Don't want to overheat my pony.

Any advice appreciated!

Coolant passages in starting engine possibly blocked. I would pull heads and check there first just because it is much easier to drain coolant and 6 bolts each head than getting to water pump.Keep us posted on what you find.

rokke17,
I have 3j 1920 I found the coolant journal in the bottom of the pony half blocked where it is bolts to main engine bell housing, this also could be a factor? if you try to remove the pony there should be stud/nuts between the rear of main engine block and pony block, ensure you have all nuts removed or breaking the pony block flanges will happen. Just beware of all the nuts holding it on

On the D2, the water pump does not do much at all to aid in the circulation of water through the pony, the pony is cooled mostly by convection circulation of the coolant, and as such the coolant passageways in the pony must be clear for the pony to cool correctly.
It is common to find them pretty plugged up on an old tractor, pulling the pony heads and cleaning out with pieces of wire and flushing with water works pretty well.
The coolant circulation from the pony to the main will help heat the main a little, but the most heat to start the main is accomplished by having the compression release in the run position with the fuel in the off position, after you have obtained oil pressure in the main, as is specified in the operators manual.
Heat is also made in the main from the pony exhaust going through the intake manifold if so equipped, I cannot tell by your serial number if yours is so equipped.
The length of time your pony will have run to build enough heat through compression to start, will depend on the condition of the engine and the temperature, an engine in new condition will start almost instantly in a moderate climate, where as a worn engine might not start at all without help from ether.