Ok so I have decided to carry this on for future Frankenstein minded people. The cognito moto trees are fitted, I'm not overly impressed with the trees as for a polished finish they are covered in machining marks and has a score running across the top tree. I will have to anodise or paint these now, also the steering stops are rubbish and I had to grind down on the inner lip to clear the steering tunnel, even with spacers on the stem, then add a 4mm rubber pad as there was not enough adjustment on the stops.
The tire issue has been solved by running a 110/70/17 on the GSXR rim and a 140/60/17 on the k1100 rim. I know I could have gone to a 160 on the rear but you will gain much more in height than you would width because of the narrow rim and this would change the geometry even more. In reality the bike has been lowered a total of 46.6 mm front and back with the the aid of the adjustable rear shock, not ideal but best I can get it, the test will be in the ride. I am interested to see how this effects the side stand issue too, should help if any thing and better than attaching a big block on the end of it.
I have also upgraded the rear disk and pads to brembo as the front now has 6 pots. Side exit exhaust fitted and just the electrics and hook up the koso dl-03sr speedo to work out.
NickHeljman thanks for the offer on mastercylinder bro but I'm going to buy the k1100rs master new, I have gone this far with it and can't cheap out now.