the 2 second buzzing sound sounds to me like something is slightly loose inside the chassis, when you moved it and opened it up, it might have knocked whatever it was back in place..
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It's no problem to run the 88 on the 4-ohm taps with 8-ohm speakers. I think you get a few less watts of power this way but also less distortion and a higher damping factor. It is the preferred way to go in many instances. Also, if you haven't already done so, you can switch the amp from its ultra-linear mode to the triode mode (with the cover removed and power off). When I had mine, I ran it with the cover off and I thought that made it sound sweeter and more dynamic. And the triode mode is more liquid and less edgy than ultralinear.
And as I recall, the Rogue 99 preamp is very sensitive to the chassis-to-shelf interface. If you want it to sound more detailed and more articulate in the bass, try it with #4 BDR cones.
As for the TT interconnets, yes, you can pretty much substitute whichever ones you think sound the best. They don't have to be turntable specific.