Ok I think I finally have this figured out from the info shared here and what I dug up. I finally got my hands on a wire diagram that had the TMAP sensor note as I purchased everything form Lotus back in 06 and recently did it again and basically everything older than 2011 is now gone so you can't buy it from them anymore and have to find it "other ways". So, with the description from the Lotus Service Notes in the MP section and after seeing the BOE instructions about the red wire going to A1 on the right side connector I finally think I pieced it together. Here it is for people doing this on their own:
The stock sensor has 4 wires and here is where they all go:
1 Yellow - RD2 - right side ECU connector. Can splice into TMAF sensor wire which is also yellow
2 Brown/Green (NG) - RA1 - right side connector position A1, currently empty and need a pin for the connector body
3 Grey (S) - RL4 - right side connector position L4
4 Orange/Green (OG) - Right side connector position B1
Now all I need is a source for the little connector pins and I can make up my own harness. Anyone know the part number or is willing to part with a few? They look like AMP connector pins 183025-1 which are used in the tail light harness but I doubt I am that lucky as I have a bag of them here. I could I guess pull one out and measure it with a set of calipers and search the 10,000 page AMP catalog again but my eyes are still crossed after figuring out the switches and tail light connectors in the car.
Quick update for anyone doing this on a 2006 Exige. You can purchase the connector body and pins from here:
Then just make the harness for the sensor and transfer one wire at a time from the black connector to your new black connector. When you are done you will have a harness that looks exactly like what Lotus did on the 07 S.