Since you already had an auto trans and an auto trans ECU in the 2007 TSX, in theory, you could have purchased Hondata FlashPro for the 2007-08 TSX, flashed in a manual trans program into your 2007 auto trans ECU and been good to go.
This would have saved you purchasing a 2007-08 manual trans ECU and you wouldn't have to tow the car to a dealer to configure the immobilizer to the new ECU.
The only negative with using the 2007-08 auto trans ECU with the new manual trans would be the lack of reverse lockout in the trans.
I could had saved money if I've known about the immobilizer. It's ok though it's a project car and I'm not in a big rush to get it on the road. Good experience and hopefully I can help someone that's plans on doing this conversation. I spent less 2k on all the parts.
Perhaps you could post up pics and details of your auto trans to manual trans swap?
Many folks would be interested, since this swap is not easy nor common.
Can you provided details on how you modified the firewall to accommodate the clutch pedal.
If I recall correctly, the mods to the firewall are the most difficult part of the swap.
The rest is patience and money for manual trans parts!