Hi Guys, Thanks heaps for the responses.
Paulr33 - The previous owner installed the PFC so I've unfortunately never had a stock ECU in the car as long as I have owned it, and the problem has been around since I purchased it (but I only noticed it happening if I didn't drive it for an extended period of time). The relay was changed, but the problem persisted - hence why the unit was pulled out and taken in for diagnostics. When Injectronics did their tests they said that the unit would start to power down and then start back up midway through the shutdown proceedure (hence why the battery was being drained as the computer starts to shut down, but then ends up keeping the fuel pump, injectors etc active). This was happening whilst the unit wasn't even in the car on Injectronics test bed (So i'm hoping *fingers crossed* that there isn't any other faults with any of the cars wiring etc that need to be addressed as well). The maps should all still be in tact.
STATUS - what suburb are you located in, I might organise to bring it down for you to look at and/or do the xfer for me. I usually just disconnect the battery manually everytime I park the car - but once I get the car back I can take a better look and maybe setup the relay if all else fails.