UPdate: Took my TTR on a shakedown ride after completing all the upgrades and it went well until a bunch of idiot lights came on. The check engine, ABS and traction control lights lit up. I rode home with no problems other than those lights and decided it was time to use my new bluetooth diagnostic reader to read and reset the problem. That is when I discovered my rearder will read the problem but not reset the error codes. Ergo, semi-useful. I then got on Ebay and ordered up an interface that was supposed to (according to the description) run on Windows 10 and was compatible with TuneECU. So after I got it and tried every combination available to get it to communicate with the TTR I had to break down and contact tech support. They offered up a lot of questions to my questions. That prompted me to break down and buy an android tablet, OBDLink LX and buy TuneECU. After diagnosing the problem with my tablet hooked up to the OBDLink LX and it was communicating withh the ECU the problem was the front wheel speed sensor. So I put it up on the lift this morning and was certain I would find too much gap between the speed ring and the sensor because I had put on wave rotors. With the bike at a convenient working height I looked at the gap between the ring and pickup and instead of too big an air gap it was no gap at all. The pickup coil was rubbing the speed ring. I slipped a couple thin washers between the mounting bracket and fork stanchion and checked the gap and it was too big, so pulled one washer and viola a small air gap. I then used the TuneECU to clear the ABS DCT code and then reset the error codes and when I fired the bike up all the lights were out except the ABS (normal until you get over 6 mph). The shakedown ride noise was different this time and the lights stayed out (progress) but it also now had a rattle. I asked Tom to take it around the block and he came back with the correct diagnosis, the left caliper retaining spring was not seated. The spring was rattling in the caliper carrier so that's an easy fix.
Simply remove the caliper, compress the pistons, slide the pads out and reseat the spring. Easy-peazy. Until the pistons won't collapse far enough to clear the pads from the retaining slots and the spring won't fit between the pistons, and when you get the spring situated the brake pads won't go back in. Other then that it was a cake walk. Finally got it all sorted and the last test ride was brilliant. No drama, no excess rattles, no idiot lights, just pure riding pleasure.