First of all you shouldn't get burning smells from a speaker cab. I think you said their was some discolouration of the fibreglass. If it isn't actually fibreglass but polyester wadding then this will singe even with speakers working normally at high power levels. You will have at least explained the smell. Move it around until it no longer contacts with the speaker. Neo's have smaller magnets so less area to dissipate heat. The easies way to test the speakers is to push some recorded music through them and listen at low volumes with your ears right up to each speaker one at a time and then with the volume up at a high level. If there is no obvious distotrion or funny noises then the speakers are ok. Have the closest look at your tweeter as this takes the bashing if you use overdrive.
I can't think of anything that would cause a loss of gain without causing other problems with a power amp though I suppose a component failure around an op-amp in the preamp stages might change the gain of a stage. Tricky to find without the amp and a circuit diagram in front of you. There are two possibilities if it is the amp, it is actually ok and you just need to turn it up or you need a better tech. Don't worry about the volume settings between the amps though, that's al about gain and sensitivity and a halfway position on one amps gain control need bear no relationship at all with halfway on any other amp. There is an excellent piece on this on this site but you could look at this too [url="http://www.youtube.com/watch?v=EbVKWCpNFhY"]http://www.youtube.com/watch?v=EbVKWCpNFhY[/url].
Again if you play recorded music through the amp you should hear any problems as distortion. If you get the chance to try this then let us know what you find