Sorry for the delay in updating my progress. I have some exciting news, but firstly many thanks to everyone who has contributed to the thoughts on this thread.
Quick run down:
1) I made an absolute buggers muddle of implementing the new decoding glue logic, so that took a while to realise
2) I only had one 74HC00, so moved to using 74LS00 parts only for decoding, with 1k pull ups
3) The output skew and peak voltage from the decoding looked weird, traced down to bad power on the decoding breadboard
4) Finally, she seemed to awaken as if all was normal:
4.1) Keyboard - Check
4.2) Video - Check
4.3) Sound - Check.
4.4) Serial - NOPE. Serial was working but only at the lower 2.68Mhz speed. At 5.34Mhz seemed to transmit fine, but glitchy receive. I suspected the 2Mhz part I am using is sensitive to clock speed and I was lucky previously, but..
5) After a little experimentation, putting smooth caps near the 6551 VDD and VSS lines sorted the serial glitch out.
6) So, back to square one but with optimised decoding logic?
NOT SO! So the obvious thing to do was put in the 15ns SRAM which was not working with the previous decoding logic. Voila, works absolutely nicely with no glitching. It was something I privately felt could happen given all the poor practices I had gotten away with in my original design, so it's excellent that taking back to reference practices has fixed the mystery.
In conclusion, the main issues with my existing design were (in order of impact):
a) Decoding logic had a lot of delay and contra-practices and using 70ns SRAM was probably masking this
b) Poor power handling e.g. need more smoothing caps across power and ground lines needed at higher clock, was probably getting away with it marginally up till now
c) Care with breadboard power and signal distribution - they are glitchy, noisy little buggers as the clock speed goes up. Having said that, they have allowed me to get on this journey in the first place, so have a soft spot for breadboard (for purely personal projects).
Many thanks again to all of your contributions - really pleased with the outcome on this one
Cheers, Dolo