One thing to be wary of is if someone left the rear retaining screw for the side plate inserted. If it was tightened down you probably would not be able to open the analyzer but if it was slightly threaded in and you open the door it can bend that corner of the plate and cause it to leak.
We have also had one instrument where the interface broke just behind the column nut and we couldn't find it until it broke completely off when trying to remove the nut.
The diffusion pump itself rarely backstreams unless you break vacuum at the roughing pump or outlet of the diffusion pump. They are designed to handle a sudden power outage without backstreaming into the analyzer chamber, but you will often see a few droplets near the pump entrance in the chamber. As for the level marks, I can't remember if there is only a level mark for when the fluid is hot, or if there are two, one for hot and one for cold. If it is at least 1/4 of the way up the glass when hot then it is ok.
Depending on the age of the instrument, there were also problems with the seal around the sight window of the diffusion pump leaking. This was in a service bulletin I believe. Newer ones don't have that problem.
As for mass 69 being high, if the calibration gas valve is open, that is one of the major peaks of the PFTBA and should be near 100% on a standard autotune. If you are tuning for BFB or DFTPP then it will be 100% and 219 should be in the 30-70% range.