So far what I know
The VIN on ECU matches the car. Based on the history and limited mods, I highly doubt that the ECU was ever swapped, so my best guess is that the ECU hardware is original. Otherwise it seems that it would be significant pain to get the ECU to have matching VIN. Car was previously not in an area that required smog, so if ECU was swapped I doubt they would have gone through trouble of sending it out to get Vin burned on.
I bought a Cobb AP V2 (too cheap to buy V3). When I connected (after updating firmware on AP), it detected the car as LGT 08-09 but it also detected as already having a Cobb Tune on it. So whatever Cobb tune was on there was over written by this V2 AP I got, but again LGT not spec.b specifically.
I bought a used AP V3 thinking that maybe it's because the old V2 (even though firmware updated) just didn't have Spec.B, but the AP V3 still recognizes it as LGT/OBXT 08-09 and not Spec.B
I spoke with Cobb several times about this. They confirmed that Spec.B is different and should be recognized as Spec.B on AP, they recognized the type of car by looking at the ROM ID, not checksum, so my guess is that CA DMV has a database of ROM IDs, and mine is reflecting a LGT ROM ID and not a Spec.B Rom ID.
The one guess the Cobb guy said is that maybe earlier in life the car was tuned with OpenECU and whoever tuned actually tuned it with a LGT Base map thus the ROM got changed to LGT (thus wrong ROM ID), so now it's just recognized as LGT.
I have 3 options for next steps:
1)send ECU to Cobb to have OEM Spec.B ecu installed, which they said they could, but that means I have to send my ECU and AP in, troublesome, although not entirely sure that is the problem for smog.
2) to the dealership to reset, although I'm a bit concerned about the dealership, they might mess more up, haha, mostly because 2 out of 3 dealerships I called had no clue what I was talking about. I would uninstall the AP and take it in
3)I am looking for someone with Tactrix Openport 2.0 cable to put the factory Spec.B rom on so the ROM ID will be back to Spec.B and hopefully AP will recognize it.
Thank you again for everyone on responding.