Tubes should not rattle and usually if something about one seems wrong, it is. Dirty pins, loose bottle, bad colors and lots of other things can cause problems or be because of problems.
Be careful because you are playing with very high voltage, capacitors store current and you don't want to get zapped. As far as the amp goes, none of the tubes are expensive or hard to find and your first move should be to decide on whether you want to keep the console or to remove the gear you would use. Then you need to get a variac, test your tubes and using a schematic decide on how you will get a signal into the amp and listen to it.
That amp should easy to work on as it has a nice large chassis. Putting an amplifying triode and an on/off switch and an RCA input along with a new set of binding posts should be easy to do, and really help you out for getting comfortable in using tubes.
I truly can not design at all, but I have built amps with spare used parts and ones bought surplus. Works too!
I would bet that one of those 5Y3s is used to power the off of main chassis preamp. Not an uncommon thing as the transformers and capacitors were the most expensive parts. The engineer was just making double use of the power supply transformer.