The floppy drive spindle motor runs straight off 120 VAC; it doesn't go through the DC PSU board at all iirc. It should run constantly and never turn off. If it is intermittent, I would suspect a problem with the motor or the AC wiring. Since these spindle motors never spin down, it's entirely possible that the bearings are out and the motor is bad. If you find this to definitely be the case, I may have some parts laying around, maybe......
If you smell burning capactors, it's probably the AC line filter (RIFA) capacitors. AFAIK (I am not a PSU guy) their purpose is to prevent the PSU itself from putting noise back out onto the AC line; they don't have anything to do with the PSU's internal workings or the quality of the DC output. I have a bad habit of just removing them and running without them, although it probably causes some RFI that might interfere with old radios and analog TVs and stuff if you are into that side of vintage electronics too. It is certainly possible to remove them and safely run without them until your replacements arrive. Again, if you discover that your PSU has bad components for which there are no replacements available or isn't worth fixing, I may have an extra one laying around, although it would hypothetically be one of the older model ones that probably can't source enough current to run all your 68k boards and stuff......
I'm not sure what to think about the video issues. Can you post a photo or video? AFAIK the analog board is compatible with the ones used in the Model 3 and Model 4. I may have an extra one, but I don't think it works.
Do you have the equipment needed to check the DC output of the PSU for correct voltage and for noise? Take a magnifying glass and check the solder joints around all the input and output pins; mine had cracked joints on the output that had to be reflowed for reliable operation. Guess I forgot about that in that previous post.
If the power rails are all ok, I would start by documenting how everything is installed, then pull everything but the z80 CPU board, z80 ram, and keyboard/display cards, but still remove and reseat those three, try it, and then put cards back one at a time (floppy controller, hd controller, 68k cpu, 68k ram) until it doesn't work again. Keep in mind as you are testing that some of the bus signals are daisy-chained through the cards, so they have to all be next to each other for things to work right, but do put them back in the same order as you reinstall them.
Hope that helps. I don't actually know what I am doing, so I hope none of that is bad info. Take anything that Pete says as 1000% more reliable than anything I say.