Your measurements sound good......but definately try lowering the trees/raising the forks.
The new shocks wont shorten your wheelbase, but raising the forks will. If frame geometrics get out of balance for the weight distribution of the motorcycle....one of the first things to notice is a chattering at the front or a worse head shake at speed. If you notice either of these you need to shorten the wheelbase. You can either run a shorter chain, therefor pushing the rear wheel forward or lower the triple clamps(raise the forks). That reminds me....how is your chain and were is your axle in the adjusters??
Also...wanted to mention....if you need any factory OEM Honda parts....feel free to contact me as I can order new parts from honda. I have a parts contact form on my website.