Day -- I believe your voltage at pin 5 of V7 is high because you measured it under the wrong test conditions (according to your test conditions in post #22). You indicated that the receiver was tuned to a station, which likely triggered the Stereo Beacon to come one. In that mode, V7 is cut off prevent all plate current flow, allowing the relay to assume its normal state with its NC contacts triggering the Stereo Beacon lamp on. With no current flow, the plate voltage at V-7 would then assume nearly that of the B+ supplying the tube, which is in fact what your measurement indicates.
I would dismiss your concerns for the voltage at pin 6 of V3. That is the screen grid element, supplied by a dropping resistor. Therefore, the actual voltage there can be somewhat tube dependent, but also definitely impacted by any IF signal presented to the tube -- received, or otherwise (picked up from ambient noise). One of these possibilities appears to be happening since the AVC circuit is apparently supplying some negative grid bias voltage to pin 1 of V3 (your indicated -0.6 vdc versus a specified -0.28 vdc). This allows V3 to draw less current, making for a higher screen voltage at pin 6. As a check, pull out V18 and see if the pin 6 reading at V3 appears to be more normal in that condition. Removing pin V18 will remove any IF signal from the front end that might be presented to V3.
As for the alignment procedure in general, follow the Fisher procedure -- other than for injecting the 10.7 mHz signal to adjust the IF strip. You're trying to mix the older alignment approach (i.e. pre-stereo MPX days) with those after stereo MPX became a reality. The older tuners used a stagger method of aligning the IF strip, and adjusting for the detector S signature because the IF transformers were of a narrower, but broad band design. This achieve the desired selectivity but made their adjustment somewhat critical in achieving a flat top IF band response and proper S curve response at the detector output. When the GE/Zenith MPX format was approved, IF transformers were redesigned with wider response (to properly handle the wider bandwidth of the composite MPX signal), but with sharper slopes at each side to maintain a good degree of selectivity. When this happened, it became entirely practical then to simply peak the transformers for maximum signal transfer at the design center frequency of the transformer (10.7 mHz). At the ratio detector, adjusting the DC balance via the top slug with the temporary installation of balance resistors has never failed to deliver a very low distortion result at the output in my experience. No modulation is needed when adjusting the IF strip in this manner.
As for injecting the IF test signal, you'll need to make a test jig to do that. The instructions were written for the original 500C offering that did not use a Nuvistor populated front end. To complicate matters, Fisher then failed to update the alignment procedures when the later (long running) Nuvistor version went into production, where then the instructions didn't make any sense since V2 then became a Nuvistor. So now a jig must be made/used to inject the signal. To make it: Take about a 3" piece of ordinary #22 gauge solid wire, and leave the insulation on it. Fold it in half. Hold the folded end in one hand, while twisting the leads together at the other end with your other hand -- but leave enough untwisted length so that at the fold, it can be spread apart slightly to make for a small opening. The twist should not be lose, but neither does it need to be super tight, either. At the twisted lead end, remove about a 1/4 inch of insulation from each leg of the twisted leads, and solder them together. Now you have your jig.
At the back side of the receiver's RF can (outside of it), you will see a short wire appearing with spaghetti on it, with a hook or bend at the end of it, and connected to nothing. This is the injection point, shown as test Point 1 on the schematic. Slip the opening in the test jig over the hook at the end of the test point lead from the RF can. The cover of the can should remain in place at all times. Connect the output of your 10.7 mHz generator between the soldered twisted end of the test jig and chassis ground, to form a loose coupling between the test jig, and the test point lead extending from the RF can. Do not try to make the generator connection directly to test point 1 without the test jig, as the capacitance of the generator connection will then alter the circuits inside the can, and no doubt overload them as well.
This will inject the signal appropriately so that you can then follow the rest of the procedures accordingly. Be sure to follow all the setup procedures noted, and keep the test signal as low as possible.
Good luck with it!
Dave