I put the 485 back in the case to give a quick run in to see if any other issues crop up. Turns out the noise on the trace was hash getting into the scope since it was out of the case. The trace is now much improved.
Issues:
Both channel 1 and 2 have gain issues. Those traces should be 0.5V p-p. They are 0.4V p-p. The gain adjustment cannot achieve 0.5V p-p.
As mentioned both 50 ohm inputs are dead.
Need to check the PSU.
The knobs on the volts/div are from a 465 junker. The originals were cracked. But the parts mule has good knobs and they will be transferred over.
I fully expect that compensation adjustments will be necessary once the channel issues are resolved.