I recently completed a manual swap on my R and the wiring was kind of confusing. Since there was no references on here I decided to post up something to help others out.
This ONLY applies for 2006 R's so if you have another year you need to download the wiring diagrams and cross reference them with mine. I don't know the differences off tops but I know the pins in the CEM are different. If you know something about the wiring for other years please reply to this thread for future searchers but most of the below should apply.
This also only works if you are re configuring the CEM and ECU to manual, not if you are retaining automatic software.
Clutch Position Sensor
So you only need to run two wires for the clutch position sensor. These wires run to the ECU and go to pin B:4 and B:15 and they are intertwined black/brown wires on a manual harness. On the automatic harness, you will already have the brown wire at B:4 and all you need to do is splice into that wire. The automatic harness doesn't have a B:15 pin so you need to get a pin from another harness and add it. If there's already something at B:15, you are looking at the wrong pin or don't have a 2006.
To count pins, count on the ECU, not from the harness. Then just reference them to the connector. Remember the red part stays on the left when looking at the front of the car.
To get the wire inside the car, you need to remove the wipers and the big plastic piece that covers the wiper motors, also remove the wiper motor. You'll see a big connector with bolts and that's going to be the CEM cover. Open it and run the wires through to the clutch switch. I bought a manual harness to use the connectors for it but you can surely solder them to the sensor pins. If you need ECU pins, send me a PM I have a ton extra on my spare harness. REMEMBER to silicone the CEM cover back to the car after you confirm everything works, it will leak.
Shiftlock aka Reverse Lockout
There isn't much you have to do there, at least for the 2006 models. There is a VO-W wires that goes to A:25 on the CEM, a BL-W wires that goes to D:23 on the CEM as well as a SB (black) wire that is ground. All of these cables are already on the connector that goes to the GSM on the automatic so simply plug the connector into the M66 shift base and you're done there. Don't put the space ball on there until you know the lockout works correctly. It should activate at 15+ MPH going forward.
Reverse Sensor on the M66
Again, nothing extreme here. There is a Y-GR wire that goes to the CEM C:28 and a SB wire that is ground. Both of these already exist on the plug that goes to the TCM so simply put them on the connector for the M66 reverse sensor. My plug to the M66 didn't have pins but we found out that the pins on the big grey connector that goes to the headlight uses the same pins so remove them from there and add it to the connector or solder them to the pins direct. The Y-GR wire goes to the left side of the connector when looking at the front of the car if the push clip on the connector is facing the hood.
The Y-GR wire already goes to CEM pin C:28 but you can confirm this by taking off the connector under the wipers when you ran the CPS wires, check to see if the same color wire goes to C:28 or whatever pin your year of R uses.
That's about it. On the wiring diagrams, SB means black wire and the rest are self explainatory. 8/134 means the reverse lockout solenoid inside the car, 3/10 means teh reverse sensor on the M66 and 7/123 means the clutch position sensor. Watch a few vids on wiring diagrams on Youtube and you'll catch the jist pretty quickly. To find diagrams for your R, go HERE.
I took pics of a few of the diagrams below, these are the ones you will want to be looking at. You can reference these to your certain model year and follow the wires and pin locations needed. I am not an expert with wiring on these cars but I spent a few hours studying the diagrams and learned what I need to for the swap and everything works perfectly on my car.
Hope this helps! Again if you know something about the wiring for other years, please post some info on it here.