I was able to spend a few hours wrenching today and have all day tomorrow to work on the stead but I wanted to post these preliminary results as this has been going on for a long long time.
I installed the 04 starter, bracket, battery box, negative battery cable and YTZ7S battery. The bike is pretty stripped down, carb off etc.
After getting all the electrics hooked up.............The moment of truth.
It works!
At first when I hit the button nothing. Leaned on it a few more times and heard a click, Humm. Tried it again and the electrics came to life. Must have been the starter relay clicking in. It has been dormant a long time.
I was ecstatic to hear that little starter spinning the motor over. I tried it again and again. It worked every time. It didn't start as the carb and stator are off but it spins good.
I used the original 01 negative battery cable that grounds to the upper chain roller and the 04 negative cable that attaches to the starter bracket. The next time I pull the battery/starter I am going to replace the allen bolts that hold the starter and bracket on (4) with regular hex bolts. There is some adjustment (play) in the bracket and it is virtually impossible to loosen or tighten the starter bracket bolts with the starter in place which is necessary to get a good starter/bracket alignment. I had to use needle nose vise grips to tighten the bracket bolts as an allen wrench won't fit with the starter in place.
Well so far so good. It looks like an 04 550/650 starter may be the ticket to better e-starting on 2001-2003 models. Especially the 01's which seem to have had the most e-start problems. Most never worked. Mine included.
I'll button it up tomorrow and see if the beast will fire up.