ok so its quite clear theres a fault(s) on this radio! The question now is, how to find it! (or them!)
It seems quite clear that since the radio is not responding to received signals correctly in frequency terms, and that after probing the AGC lines its clear that the AGC is not reaching anything like its correct levels, that going immediately for the manuals recommended alignment process, which starts with the AGC, is likely to be futile.
I think first I should look into the odd frequency problem. I know that I can receive at 5.450MHz but not seemingly at 5.505MHz, so I will start here and see if I can work out what is actually happening. Its possible that the data-contention diodes, even being low forward voltage Schottkys, might be causing issues with low volts on the synthesizer pins, in which case I will need to add the extra 3v regulator to allow me to bump up the 3v line to compensate.
However, with the odd frequency issue I suspect its going to be something else. As it effects Tx as well as Rx, I think I can rule out the RF side between antenna and the VCO controlled frequency conversion.
This is a very complex radio, but when alls said and done, its still just a superhet!