Transformer has been checked/megged by outside company and passed. It is dirty. I believe it's a moly heat zone. Motor/fan has both been replaced a couple weeks ago. I didn't personally see what it looked like inside. I'm off this week, so I can't verify some of these things, nor am I normally involved in maintenance of the furnace. I did hook up a different motor on the floor and it did start normal. I think it has been determined that the transformer makes that noise under a large inrush current under heavy load, was told we had a normal contactor and noisy starts were normal back in the old days. Now Im starting to suspect dirty heat exchanger/debris/faulty butterfly valve. It does seem to start up and end up tripping an OL breaker we have post transformer at the motor. Watched the current rise after it should have been on it's way back down.
I wouldn't suspect butterfly valve (you mean the backfill valve or the heat exchanger water valve)?
However.... you may want to check the flow switch on the exchanger water flow. It may be intermittent.
I am serious about checking the vacuum tight power connections that carry the motor power thru the exchanger can. They can short out across the plate on the inside and the power connections are pretty close together. Are they Auburns (look like a large spark plug)? When you inspect this plate...look for arch flashes on the back side of the plate and inside the pipe.
Some if these systems used a junction block mounted below the motor. The motor leads went from the vacuum tight connections to this junction block consisting of 3 connections with high voltage insulators. If it exists I would check it out and maybe replace the insulated connectors.
What is the HP of the motor and the KVA of the transformer?
Now..... I use only a transformer specifically wound for drives (Drive Isolation Transformer). We do a lot of cooling blower systems with VFDs.
https://www.hammondpowersolutions.com/product/hps-drive-isolation-transformer/
I have also done a lot of systems that run the motor at 480V. I can do this overseas, but in the US "NFPA 86" prevents me from doing this...
3-10.3 Fans and Motors for Gas Quenching Systems.
3-10.3.1 Fans shall not be exposed to any temperature in
excess of their design temperature rating.
3-10.3.2 Electric fan motors shall be interlocked to prevent
operation below a chamber pressure of 7 psi (48 kPa) absolute
to prevent motor failure.
3-10.3.3 Where motor windings are exposed to argon gas or
other ionizing gases, the voltage on the motor shall be limited
to 260 volts maximum.
If you run Nitrogen only....you can go 480 on the motor.