Hunter,
Cal is right about the flex. The 550 has a stamped frame and the frame welds are not very robust. It would not be a bad idea to reinforce the welds to the head stock. If you have access to a welder, you may even gusset the triangle areas of the frame (see the circled areas below). It is not necessary, but it may help. Just know that when you strengthen portions of the frame, you will be highlighting the weaker areas.
My comment about checking the weight and re-springing is something to look at upon completion and tuning, since you'll then have an idea as to how the finished 550 compares in weight to the particular GSXR model you took the fork from. It may end up heavier, lighter or a wash.
As for the bar mounts, Devin at Cognitomoto sells them. I would not be surprised if you purchased a top clamp and the risers if Devin would not tap the clamp/mount them for you for a little extra. Devin is a great guy to deal with.
http://cognitomoto.com/collections/cockpit/products/rise-clamps-7-8-bar