Fuel dumping when starting fuel dumps into the system and also into the oil system

Sorry I can't help with the transmission whine - you need to get an experienced somebody to take a listen.

Your description of the oil problem suggests a blocked crankcase breather system and in particular the flame/oil mist trap. I have encountered several with the same problem where a pressure builds inside the crankcase and it pushes oil through the breather, in one case emptied the oil pan into the air cleaner and ruined the vortex counter (air metering unit) and other times oil beginning to seep from almost every seal and gasket.

Does your car have a diesel particulate filter? Is that what you mean? If so your first question should be, is this the right car for you? Cars with this filter do not cope well with lots of short trips and no 50+ mph runs. These short trip will make the filter full and it will need a regeneration, a high rpm 50+ mph run or a for regen at a dealer. The filter may be ruined already. If so it will dump diesel in your engine oil. The system uses diesel to burn off the soot. If the filter is faulty/ bad this extra diesel will be dumped in your engine oil. So check the oil level ASAP, as the extra pressure from the high oil level can kill your engine.

Fuel pressure regulator. or stuck open injector/s. The only way gas can reach the oil is threw the piston rings. Gas will seep threw them. regulators can dump a lot of fuel threw the plenum. An open injector will bleed off pressure(when turned off)) and dump gas right into the piston.

If it's "dumping" fuel into the engine, the computer has it cold start mode. Stay off the throttle pedal when try to start after a good while to allow fuel to clear. If it won't start then, you've a fuel regulation problem on cold start. But do wait a good while for fuel to clear fron engine, then try to start without touching the throttle. It's meant to be this way.

I would start there way to much pressure at separator check fuel pressure you may want tto try a good additive seems like there is alot of condensation

Electrical problem. Something gets hot and stops working. Could be fuel pump or something in the ignition system, so losing spark. After it stalls, spray starting fluid in the intake and try to start. If it fires up and runs a few seconds, you know it's a gas problem. If starting fluid doesn't do anything, check for spark, it's probably an ignition failure-possibly the coil or the ignition control module. The module can be tested at a parts store.

Did you use the injection system from the other engine or the one that was on your old engine?If you used the one off the old engine the injection system may be bad and that is why old engine was knocking.

Unlikely it's the regulator causing fuel to be dumped into your oil. A stuck open or leaking fuel injector would dump fuel into your oil.

running rich, check for fuel injectors leak

dump where? gas tank ..carb?..look for cracked fuel lines from tank to engine/fuel pump