speak to Dave Harris (on this board) or Neil Spalding from Sigma, I was speaking to them earlier this year and I believe Neil can now get "blank" ECU's if thats any help and Dave was involved with this subject too - remapping blank ECU's - not sure about the "de-coding" of existing ECU's - I believe that this was proving to be very painfull.
The power commander will only override the fueling on the ECU.
FIM are developing a fully programmable ECU for the 999 range, I think some test versions exist - Neil Spalding has one I believe - but these will enable you to change rev limits, fueling, swap from race functionality to road functionality but may be cheaper than a replacement Ducati original part, eg Pro-Twins offered me a Ducati Corse ECU - fully programmable but it costs the best part of £1k
there isnt a chip in the actual egnition, the chip is in the black cowling around the egnition so if you have the key why cant you just tape the key to the cowling and run a switch??