Hello 80GS1000, I have an 82 GS1100E that I am doing the same mods to except I have an 95 GSXR1100 front end and a 2005 GSXR1000 swingarm. Did you get the swingarm spacer in the middle machined as well? I have my new swingarm pivot spacers made already and would like to know basically the steps for figuring out the correct location to weld the upper shock mount on the frame. Did you first set the head angle then go from there.......I've seen the suspension geometry links you have provided but what I'm looking for is what steps in what order. I believe you start to get into it on pg 28. Sounds like I need to put the engine back on to get the numbers right? Could you possibly share you're measurements and specifications for the monoshock mounts.
Any information would be helpful.
I did notice several others have done the same thing and ANY assistance would be greatly appreciated. Thanks
First off, cool bike! The mods you have planned will be a great improvement for turning and stopping.
So, to answer your questions...
Swingarm spacer in the middle is not machined. The trick with the swingarm pivot spacers is to make sure that they allow for the swingarm bearings to work properly. You want the rotation to be in the bearing, not the pivot bolt to rub on the pivot spacer to prevent galling. When you assemble everything, grease up the pivot bolt and the swingarm bearings well.
What material did you have your spacers made from?
What size rear wheel are you using?
These steps worked for me to determine the correct placement for the shock mounts
*:
1. Go find a 2005/2006 GSXR 1000 and take lots of pics and measurements of the swingarm angle, the linkage angles, chain clearance above/below the swingarm, and the shock angle. A dealership with a used bike is ideal for this unless you have a friend with one. The idea here is that we're copying Suzuki's ideal configuration for that set of rear suspension components.
2. Put your motor back in the frame. I know this is a pain but checking chain clearance is very hard with an absent motor. Hate to tack all those mounts in and then find out the chain clearance is all wrong.
3. Slap a
magnetic based inclinometer (under $20 at Home Depot) onto the headstock to measure the rake angle. Put bike on a motorcycle jack like the one you have, jack up the rear till the headstock is 24.5 degrees of rake.
4. With the bike up on the motorcycle jack, adjust the rear suspension components (swingarm, linkage, and shock) until they are at the specifications you reverse-engineered in step 1. Check for chain and ground clearance once you have it mocked up where you think it needs to be. Once you have all the factors dialed in, this tells you where in space your monoshock mounts need to be. Precision, precision, precision.
5. Build your mono mounts and weld them to the frame based off the spec you determined in step 4. Take design hints from existing GSXRs - those engineers know what they're doing. Also see YoshiJohnny's new thread on OSS. Check, then tack. Check again after tacking before welding it in solid.
6. Brace the frame.
The X shaped bracing and the tube in the V of the bottom of the subframe is highly recommended to manage the new forces introduced into the middle of the frame.
I'm probably forgetting something so if you have questions, shoot.
*Remember this is all at your own risk/discretion and if you don't trust your welding/fabrication/engineering skills with your life (seriously!) farm out the work to a pro or just buy a stock monoshocked bike*
imo all you need to do there is either sleeve it to the size of the spindle you are using or replace it with one of the correct length that fits the spindle 
