Hi Gary. To be fair to you and the kit, the bolts you supply would be 100% ok, but I have the Yamaha trunk and mounting plate to install, hence the need for the longer bolts. Again, totally nothing the kit should have to address. If I weren't mounting the trunk baseplate, the supplied bolts would be just fine.
Regarding the holes, it would've been fine as is, I had a tough time getting the Stiffy kit to "stay still" while I was tightening the L brackets. If it shifted slightly, the holes were a little off. More than likely, it was user error on my part since I'm still learning my way around the FJR.
I picked up a couple of small bolts that go in the plastic center section of the tail, to bolt it to the two side pieces, so I'm thinking I should be good. Once I get the longer bolts, I'll install the trunk. I ordered some 70 & 80mm long bolts. Like I said, the ones supplied in the kit would most likely be fine, I just wanted to make sure I had plenty of threads to hold the trunk baseplate on. I think the longer bolts that were holding my trunk baseplate on are 65mm, so I just needed a little more. The longer bolts in your kit are 60mm, you are correct.
Thank you again for the speedy service and top notch workmanship on the kit and the instructions.