Okay, I'm going to post my diagnostic procedure, and see if anyone has a problem with my thinking.
I think I may have figured out the problem, although I have yet to finally fix it. J2, which is up against Q46, appears to have been touching the anode of D90. If I am following things correctly, it appears this has brought the emitter low, instead of letting the diode shunt only any negative voltage to ground, which explains why I was getting absolutely no power after I changed the finals.
I'm still getting very low power output though. I'm only able to get a maximum of 5 watts RMS. I am also only able to get about 10 watts from SSB. When I go to bias it, I can get amperage for the driver between TP1 and TP3, which I set to be at 45mA, but I got no bias amperage reading between TP2 and TP3, so I turned it up to 55mA with the same results.
I also checked the voltage at the finals, considering that since I am not getting any amperage that there may not be voltage getting through. In RX, the collector voltages of the driver and both finals are supposed to read around 4.15 V in AM. I am getting 7.40 V on the driver and both finals. The base of the driver is supposed to read around 0.740 V on AM TX, and I am getting 0.257 V. The base of Q46 is reading a negative 0.965 V on AM TX when it is supposed to be +0.68 V, and Q48 is -1.7V when it is supposed to be +0.58 V.
Since I'm getting negative voltage readings where they should be positive, I assumed I may have a bad diode. The only two diodes close are D90 and D91, so I checked them. D90 is acting very strange. It reads as a diode sometimes, and reads shorted at other times. I've never seen that happen before, so my first assumption was that I was screwing up my connections, so I disconnected both sides and tested again, and similar results appeared. I'm going to assume it is bad. D91 doesn't conduct at all, which I am able to be confident means it is bad. Both of these diodes tested fine when I first pulled them out to change the finals, so that short must have done a number on them.
So, I guess the question is, should I locate some MV1Y diodes that are already affixed to the copper heatsink, or is there an easy way to fabricate something with a 1N4148 or 1N914 diode that will dissipate the heat? I'm assuming that's what these are. Maybe I can just mount a 1N4148 a little higher on the copper with some epoxy, and leave the old one in place and cut the leads off of it?