Just to be clear the order of things that I posted worked for me, at the time I had a Haynes Manual (online, since expired) and I'm pretty sure that it said lock the trans down to the trans plate first. I didn't agree as i posted before. For the record when I got the FXWG it leaked like a sieve and a previous owner had put about a tablespoon of silastic around the bottom of the inner primary where it meets the engine cases, to which I thought why?? Is there a big alignment issue here somewhere?? it also wept a very small amount of oil around the bottom cylinder gasket, and I noticed that when I undid the top motor mount to frame it seemed to have some preload and the thick spacer was a non-genuine alloy block that I could see was hand made.
So, to explain why I did that mount before the head bolt mounts was so I could be sure the two lower connections on the head were free floating so to speak.
Why did I align the rear wheel. well apart from the things I mentioned above already was the fact that this bike was 30+ years old with an aftermarket engine. (S&S) and God only know how many people have had their hands on it before, and was the frame even straight?
I know the trans plate wasn't, it didn't sit flat on a glass plate, it was chrome, I had that striped, I straitened the plate in the press, got it powder coated and then sanded it on the glass plate till it sat flat. I also a had striped receivers on the rear where the trans plate bolted to the frame and had to drill tap and put nut certs in. pretty sure those both or at least one of them had the wrong thread type bolt in it.

Now again why the Wheel alignment? I didn't want to get the motor, trans and inner primary all pulled together and tight to the frame to find out that the front pully was cocked slightly to the left or right. additionally, prior to pull down my belt tracked to one side of the rear pulley (aftermarket). it could have been the spacing on the pulley to hub, but I didn't know this either. As part of this rebuild, I refitted the original rear pulley that I had customized (see image below). So it just made sense to me to start on the back wheel and get that square to the swingarm in the position that it would live in when reassembled and running down the road. What interested me in the original posters post was his motor is or was (old dyno sheet) about the same HP as mine and from what I had read and was fearful of was what has happened to him, might have happened to me.
I totally agree with the loose bolts, I just thought that was a given but undeniably it was the torque twist allowed by the loose bolts that broke the inner IMHO.
As I said earlier this bike leaked a lot of oil and I have posted on those fixes in my previous posts, oil tank, trans main shaft and quad seal, outer primary seal/gasket. This bike is currently sitting in my lounge room and does not leak a drop. I ride it and get on it.
All are my fairly recent practical experiences, did I do exactly what the manual says, no I didn't, I replaced course thread with fine and torqued things higher than factory spec. Did I do anything that would compromise the integrity of the build? i don't think so. in my opinion and that's pretty much all i have is that i went over and above.
sorry for the long post.

 

Follow up. Found some issues inside the case. Rotor separated from the splines. Stator was hanging on with 1 bolt in place. Maybe the rotor broke free and smashed into the case? At best it was intermittently spinning against the primary cover. Notice the black vs silver from this past fall to last weekend. Need to address the starter housing as well.

Good rotor last fall


Bad rotor last weekend

 

Usually the compensator nut loosens up allowing the rotor splines to be eaten away by the crank sprocket shaft.. You will need to check crank run out at this point.. take it to a shop if you have to..
As for the starter I would get an upgraded 1.2-1.4kw starter.. Believe All ***** had em..

 

I just put a new compensator and chain on last fall(?). It took more effort to get it off than it did to put it on. I believe the comp nut was good but I've obviously been wrong on some inspection issues just within the last week! I had to google run out... It looks like the tools will be much more affordable than to taking it to a shop. Especially so considering the current state of disassembly. The plot thickens on a daily basis...

 

I personally don't have any tool to slip over the sprocket shaft to check the run out at that end.. it's usually checked in close to the wheels and I believe the max run out there is .002" . This might be one of those things that a shop should check, at least that is what I would do.. Maybe someone else will chime in..

 

Deleted, already covered.

 

Prior to my last post I did a quick search on run out. I guess I'm not sure what that is. I thought is was the amount of wobble in my output shaft. I saw a tool I thought would measure that but it looks like it's just for measurement on the shaft from the cam chest side. I don't know if that gives me any relevant information for my issue. I don't understand what could or would be checked close to the wheels. I'm thinking wheel/tire. Am I miss understanding wheels? Would you be willing to enlighten me?

 

This won't directly answer your question but I hope it helps you out.
Wheels = Crankshaft Flywheels.

 

Thank you. Makes sense. Much more involved than I was thinking or more likely hoping it was.

 

I lost about a month of summer riding but I got her back on the road a couple of weeks ago. Just like my rear shocks the 87' is difficult to find some parts for. I couldn't get an aftermarket case and I got scammed on the internet trying to buy a used one. I ended up having mine welded. I made a couple of mistakes putting the primary back together so I had to do that three times. She currently runs and drips in the garage at a familiar rate!