The problem with the Onkyo sounds like it's related to the internal amps. The bass is coming from the sub through a sub pre-out (not using an amp inside the receiver), therefore isn't affected. You could add a separate power amp, but I'd be worried that the receiver's problems could get worse if it's already experiencing problems. The SR5005 would probably be a very good replacement for it.

What sources do you have with the Sony TV downstairs? If you're losing HDMI inputs, an option could be to use an external HDMI switch - or, if you only have a couple of HDMI sources, the 990's DVI switching. That all assumes you are able to keep at least one HDMI input working on the Sony, though...