make sure the engine exhaust system does not contact the chassis in any point. If you use a hanger for the exhaust to drivetrain, tie it to the trans crossmember like a factory mount (use the same sort of bushing the OEM uses).
I think you are having two issues. One is the mounting/vibration/noise related to the way the trans and exhaust system is mounted.
The other, resonance/vibration at specific RPM under load sounds like a pinion angle issue. The trans tail shaft and differential input flange need to be at identical angles (equal and opposite), with the trans higher than the differential so the driveshaft has a downward slope.
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