[R-390] R-390A help needed

[Bob]

I have been cleaning and working on a Stewart Warner R390A sn65 for the past
year. So far I have disassembled, cleaned, and replaced broken parts in the
RF deck. Replaced all paper and electrolytic caps, gone through the
alignment of the mechanical and electrical components. Replaced 7 bad
crystals in the crystal osc. I also replaced many weak tubes.  My problem is
that I have never seen an operating R390 to compare with and my training is
mainly digital so I look for a signal to be there or not. I am not familiar
with troubleshooting stage gain. 
Current state of receiver:

1.	All stations receive about 3-5Kc high as read on radio.
2.	All received signals have low audio, both from Local Audio and
through the IF BNC connector in rear of rec fed into a separate amp. This
also happens when the Signal strength meter reads a 40-50 db signal.  I can
feed a 3 microvolt signal into the ant in jack and it is loud enough to zero
beat.

My question is how do I approach troubleshooting this?

Thanks,
Bob Fay WC0D