Not many new findings, had some other things going on and haven't been able to work on it. I verified the ground coming off the stator is functioning. Got a second opinion from a friend, he pointed out that I used a fairly liberal amount of dielectric grease on the VR/stator connections, probably too much. Also some of the grease was separating - forming a part gel/part liquid substance. I took the connections apart, cleaned them and the sled reacted well to it. Idling normally, running more consistently, codes all gone. It had some hiccups on a test ride still. Before going to work today I did a bit more thorough cleaning via blowing them out with connection cleaner and I am letting them air dry. When I got home tomorrow I'm going to take the tank off and go though the rest of the wiring harness looking for chaffing.
I'll explore the codes, however, I never had codes prior to this pull cord issue, I'm leaning towards the codes being associated and solved with this electrical problem. My timing sensors were pretty jacked up so I'm fairly certain that explains the P1004 code. ISC was probably confused because it wasn't getting accurate readings off the flywheel. 1003 (oil pump outlier) and 1005 (low voltage) I'm guessing lead back to stator function, or lack of.
Obviously I'm not a technician, but these are my thoughts and gut feeling. All opinions and advice is welcomed and much appreciated. Thanks all!