The 1.3K resistor may be toasty but it's unlikely to be the source of the problem at hand. You can rule it out by looking at PHOTO I instead of the 2nd harmonic. If the photocurrent remains steady while tapping on the unit, then the problem is unlikely to be associated with the lamp.
Once the covers come off, the first order of business is to check the various SMC coaxial connectors on the bottom of the chassis to make sure they are tight.
It's a closed-loop system, so a good second troubleshooting step is to open the loop, and there's a switch on the control panel for just that purpose. After you familiarize yourself with the block diagram, check out some of the documents published by
Corby Dawson and others for some good test points to monitor with a scope.
Another suggestion: switch back to closed-loop mode and see if you can tell whether the problem is in the OCXO versus the rest of the loop. (In an updated unit at least, the OCXO is right next to the RVFR; you can't really bang on one without affecting the other.) Compare the 5 MHz output to a known-good source with a scope, either in X/Y mode or simply by examining the two traces directly. When the glitch occurs, does it ring down or recover immediately?
If you can't tell anything with the scope, tune an HF SSB or CW receiver to 5 MHz and listen to the tone you get from the output jack when you tap on the unit. It should remain rock-steady (at least from the perspective of your ears.)
In either case, if the signal breaks up with a burst of fast static or jumps rapidly on the scope, the problem is likely in the OCXO or one of its power supplies. If it comes across as a slow, subtle tone shift or artifact, the problem is more likely ahead of the integrator. You could confirm this by pulling the integrator board.
Also, wiggle all of those SMC cables while monitoring the scope or receiver. They can and do become flaky.