LS1 powered Cobra

I hope to buy flash scan in the next couple of months to start tuning the LS1 in my AC Cobra.

I'm working on the engine loom at the moment which is a factory Holden Commodore LS1 M6 engine loom. I'm not using a BCM and plan to just run the ECU with VATS disabled. I've got the OBDII connector and loom out of a VS commodore loom and I'll graft it into the LS1 loom so I can connect flash scan.

I've yet to buy an ECU and I'm wondering which one to buy. My local Commodore wrecker has a few LS1 ECUs to choose from. I've checked out the thread on the difference between ECUs so I can tell them apart.

The thing I am wondering is does it matter if I use an ECU from an auto equipped car with my manual gear box LS1?

Can I overwrite the flash image in it with another tune ie the M6 GTS300 tune from the Stealth V web page as a starting point?

I just bought a Wideband O2 from Tech Edge. These guys seem to be pretty good to deal with and were happy to answer all my questions. I bought the 2A0 unit and it looks like it's do the job.
Here's a link to the 2A0 unit I bought http://wbo2.com/2a0/2a0.htm

Thanks

Obviously, you want a '99 or later style PCM. As for the PCM itself, it doesn't really matter whether it's from an automatic or manual trans vehicle-- as long as you reflash it with a manual cal or make whatever changes are necessary to eliminate error codes related to an automatic trans that isn't there.