What you're telling me on the rear panel jack & XLR Direct Output problems tells me that your amp has numerous solder fractures across the rear panel of the main PCB. That PCB is supported entirely by the solder joints of the two bias pots, the three phone jacks and the XLR connector. Even if your two heavy transformers (PT & OT) aren't loose, the sheer weight of them during transit is enough to inflict breakdown of the solder joints of those connectors, and probably the two bias pots. It is a very common problem with those amps. And, if the bias pots have solder fractures, you have potential problems that can cause tube failure and worse, though the protection circuit will save you before it gets too far out of whack. The sound you're hearing during power-up may well be from solder issues, so let's start there and get all those under control first.
Besides the solder fractures on the Cliff phone jacks, they also suffer from tension problems, where the normal no longer is in contact with the bar contact. Sometimes they can be re-tensioned, sometimes not.
I don't know if you have the technical skills to tackle this amp. But, if you do, and haven't ever pulled one of these amps apart, the preamp has to be removed first, then making a note of where the two 2-wire cables plug into (Blue wires on left, White wires on right) at the far left corner, and where the red stripe is in the middle, so that doesn't get installed backwards later, you pull those cables free, release the ground wire from the rear of the chassis so you can fully remove the preamp. Then, five chassis screws from underneath remove the power amp chassis. Pull it out of the case.
When I know up front you already have this much going on, I'm pulling the power tubes out, labeling each with a Sharpie as to their tube position, so you have a good starting position when it's time to re-assemble the amp. I pull the power tube plate off, then remove the power tube PCB for inspection, while with it out of the way, you have access to the component side of the main PCB.
If your output transformer is physically loose, two of it's mounting screws are not accessible without removing the main PCB. You don't have to completely take it out of the chassis, but it does have to be lifted up out of the way to gain access to those screws, to re-tighten them. And, assuming there are solder fractures on your preamp out/power amp in and slave jacks, as well as the bias pots, the PCB has to be out to have full access to do the repairs. De-soldering and re-soldering is the normal procedure, rather than just applying more solder. 60/40 solder works best, better than 63/37 tin/lead content. Forget about lead-free solder.
The XLR connector pins are fractured based on what you've already told us. They ALWAYS fracture. Any doubt, have a close look under very bright light and magnification. I wear surgeon's fiber optic headlight and focusable loupes to fully see all this (as seen in my avatar).
I'd also venture a guess you have solder fractures on the front panel pots' PCB mounting. You're going to have to go this far in for correcting the amp, so might as well go all the way and get another five years or more trouble-free service out of the amp while you're at it.
Also, you will need to lift out the Output PCB assembly to inspect the pair of phone jacks, the Neutrik NL4 connector and the Impedance switch, as well as the feedback and transformer input socket. Solder fractures are common on the jacks, as well as on the switch. Both ends of that two-wire feedback cable's connectors often are fractured. And, on the main PCB, there's two connectors along the rear edge that regularly fracture....the preamp's mating connector....5-pin header, and the connector from the heater/screen supply power xfmr. I nearly ALWAYS find solder fractures on those connectors.
Then remove and lift out the AC mains PCB assembly. Solder fractures on the IEC connector pins, as well as on the fuse holder connections are also very common. Underneath each of these two boards are one of the mounting screws for both the power and output transformer.
If the amp has been in service for years now and hasn't been to the shop, I'd also be looking close at all the solder joints of the filter caps on that main PCB. As well as the solder joints on the driver tubes & input tube on the main PCB.
While you have the power tube PCB Assy out, make close inspection on all of those tube sockets and square pins. usually the 1/4" Faston terminals are ok on these amps...I've rarely had issues with them. Also, check to see if the screen resistors are 220 ohm, and not 22 ohm with diodes in parallel with them. Not to be confused with the two series diode strings across the OT's primary to GND. 220 ohm 1/2W flame proof resistors are what is called out, though I use small body 2W metal oxide 220 ohms in my service work.
That's enough to get you quite busy in repairing this. There's more, of course.....depending on your technical skills, so let's see what you've found first. Working on Ampeg SVT's is NOT a simple task....it takes a commitment to tackle a brute this size. I work on them all the time so I do have it down to a routine, somewhat. Best of luck