Hi Tim,
I'm not aware that there is any aluminum in the heater core itself, only the housing & support assembly. Vinegar shouldn't hurt the inside tubing. I doubt if it will do much good either.
When I first got my BN2, the heater was bypassed. I checked it & found the water passages were plugged solid with bees & rust. I pressure flushed the core with a garden hose & got a lot of junk out. Connected the heater, refilled, & it dripped on the carpet. Leaks in the core, which was likely the reason it was bypassed in the first place.
I disassembled the heater, some really curious wire routing, & odd assembly with clips involved. My local radiator shop was able to fix the leak, flush, & presure test it. They said that if the leak had been in any other location it would have been impossible to repair. Moss offers a replacement core for something like $525.
The heater isn't easy to remove. There are three mounting studs, two under the dash in a hard to reach location, & a third lower stud that is accessed from the engine side of the firewall. Hidden deep inside via a rubber plug in the firewall.
The fan motor bearings were also in dire need of help. I hope simple flushing is all you need. Going further can be a real adventure.
The good part, it puts out a surprising amount of heat which is welcome in my winter sub freezing climate. With top & sidescreens buttoned up, it can get down right toasty.
D