Tony, with respect, you need to spend just as much time and attention to the set up, configuration and tuning of the ECU as you do with the engine itself. I spent two weeks on my first attempt to get the Mini running with Vems, and likely another two eeks messing around with the tune, not to mention the 2.5 hours on the dyno.
It sounds like there may still be a few gremlins in you set up, even though you are up and running on 1.1.44. Believe me, 1.1.44 is far better than 1.0.73 in many respects, but 1.1.74 is far better than 1.1.44. You need to spend the time working through the problems.
If you really need a running car and don't have the time to mess with it, don't mess with it, even though it desperately needs upgrading.
I would personaly use a tacho that works direct from the coil, where possible. I know Rover used this method.
Just trying to help, as I feel your frustration, and it reminds me of my beginings