I can't speak on whether your amp is safe to keep using or not - I suspect that it is, but I'm not a tech. The sounds you describe don't seem to be way out of the ordinary, however. Tubes sometimes make funny noises and smells when they get hot or cool down - especially new ones. Did you reset the bias and balance when you installed your new power tubes? What kind of power tubes are they? Are the little lights on the back of the amp glowing green or red?
To test the pre-amp tubes for microphonics, just take the metal tube protectors off and tap the the tubes lightly with a chopstick or a drumstick with the amp volume very low. If you hear a heavy "thunk" sound or a ringing sound, chances are you have a bad tube. Same thing goes for power tubes.