You do need to check that before you do more esoteric troubleshooting. If the 3.8 GHz oscillator is off, then for a given YTO frequency the IF will be off too. Too much IF error, and the YTO loop will not lock.
I have to mention that the 3.8 GHz oscillator has a varactor inside. This varactor is used to move the cavity oscillator's frequency slightly, depending on the programmed source frequency. As I mentioned in an earlier post, this is done to avoid some spurs. Every time the firmware shifts the cavity oscillator's frequency, the YTO gets moved by the same amount and that keeps the IF at the right place. For this reason, you can't just attach a counter to the 3.8 GHz oscillator and adjust it. It's frequency is dithered, depending on the desired source frequency. So, you need to do test 54, either with a filter, or using the more tedious method which I think is described in the manual. The filter is not critical in the sense that you don't need the exact HP/Agilent part number. It just needs to have a certain stop band. The manual probably says something about it.
Vladan