Thanks , I want to address each of your responses:
Yes the Swingarm isolators are indexed on the pins correctly.
Yes, I use the recommended tool from the FSM to correctly align the rear wheel in relation to the swingarm pivot. I made one and purchased another from Motion Pro. This was done before anything else.
The Michelin Commander II front tire is so much wider that the rear it does make things harder, but it can be done ( and I did it.)
To make sure the handlebars were pointed perfectly straight ahead I measured from a fixed point on each fork ( bottom drain bolt ) to fixed point on the frame on both sides and adjusted accordingly. To get the back of the bike in line with the front I started with the eyeball method, then used an 8 foot straightedge to square it up as perfectly as possible.
Instead of using bubble levels or the lasers which both turned out to be problematic I used magnetic base angle finders (3) one on each disc and one on frame to determine 90 degrees and 0.
My bike was not set up at the factory. Early in it's life it was involved in an accident which required frame replacement, I purchased the bike right after this as a roller to build the current bike. Unfortunately on it's first test ride after spending a winter building it I had a Buick station wagon turn left right in front of me, again bending the frame and forks. Frame replaced again at same dealer, guys insurance paid for all the custom parts like wheels, brakes etc. During the frame swap the second time I had many issues with the quality of the work performed at the dealership, lots of loose nuts and bolts and just sloppy work in general. I've been attempting to make it handle better ever since.
After re-checking everything again and starting from the beginning again, I was finally able to get everything into near perfect alignment, no more than .5 degree off in any plane. The top and front adjusters required lots of adjustment to get it right but now the front engine mount is seated correctly and everything is in alignment.
I am a perfectionist and have been known to obsess over details to the point of affecting my mental health. I am confident this time it is as good as it can get. And i'm tired of messing with it.

 

That's what I call a "complete" answer, thank you!

I always say, doesn't matter how you get there so long as the finished product is near to perfection as humanly possible. My compliments for staying with it. 👍

 

Thanks, persistence does pay off, although some people would call it just plain stubbornness.

 

I just wanted to update everyone who has been following my braced swingarm build and spherical bearing install on my 88 FLHS. After years of chasing a weave I've finally got this thing to handle well. The combination of the spherical bearing swingarm kit, the braced swingarm and the already installed Glide Pro swingarm mounts and axle, Glide Pro front engine mount and a thorough alignment the bike tracks beautifully. Even on bumpy, patched, cracked up sweepers at illegal speeds it tracks without wagging it's tail and is much more confidence inspiring. The whole bike feels more solid, more like a unit. I was a bit concerned when I first fired it up as I noticed the engine wasn't flailing around in the frame like it used to and I thought I was going to feel a lot more vibration but an all day 160 mile test ride proved I had nothing to worry about. Finally a solid feeling ride. worth the effort.

Suspension set up:
Front forks: Race Tech emulators, Race tech springs, Bel Rey 12wt oil.
Rear shocks: DS adjustable length premium set at 13"
Braced rear swingarm with spherical bearing kit and Glide Pro mounts
Custom third link
Rolling Stock:
RK Excell chrome Aluminum 3.5" rims, Buchannan's polished SS spokes, Ness billet aluminum hubs. Michelin Comm. II stock sizes
Front brakes PM 6 piston calipers with EBC floating rotors, PM master cylinder. Rear stock rebuilt caliper and master, floating Harley rotor, braided SS brake lines F+R

 

String trick on the wheels is not going to work, since HD did not put the front and back wheels in the same line until 2006 on the touring bikes.

The power train alignment tools get you in the hunt very quickly to begin with, then you can tweak from there as needed.