Read this link about riding position:
here. It may help.
I've hated just about every new bike I've ever had - for the first few weeks. I hate the color, I hate the way they sit, I hate...
New bikes suck, when you start riding them. Give it some time. 100 miles in 5 days barely qualifies as a test ride. If you don't rack up more miles than that in a week (not that there's anything wrong with that - riding isn't a competition), it may take you a month or more to decide if you can adjust to your new bike.
Coming from a scooter to an FJR is a serious change. Once again, give it time. An FJR isn't as easy to ride. It's not a scooter, and it's not a cruiser - but it's not a pure sportbike, either. It isn't
that hard to ride; just takes some adjustment. ST bikes are serious distance machines. That means, they're comfortable. The riding position is very different from average bikes, however... But then, an FJR isn't an average bike.
If you can't flat-foot you bike, you might consider having it lowered. Others have, and still others deal with the height. One-footing it, or tip-toeing it is okay, providing you can do it, in comfort. Once again, give yourself time to adapt. If that's part of the problem, a boot with taller soles could be of help.
Crowd the tank, don't tense up your arms too much, sit upright with a slight forward lean, and it might not hurt to exercise your thigh muscles. Some riders do squeeze with their thighs - I find I don't really have to, unless I'm twisting through a lot of curves, but - whatever works for you.
Many people complain about adaptation or ergo problems with their new FJR. Would handlebar risers help? My bike was killing me, too. I about died on my first 5-600miler. I got a set of risers (instead of getting rid of the bike), and found I didn't need a custom seat, or anything else. Risers fixed my ergo problem. There is usually a solution to these problems; stick with it, and you'll find yours. I would advise, however, that you give it some time, before you begin spending money. You could discover all you really needed, was sufficient saddle time.
Give the bike and your body several hundred miles. Then, decide if you need something to help out. If nothing works, don't feel bad. It's a fact of life that not every bike can be made to fit everybody. Most find a solution with the FJR, but there's always the outside possibility that you may not. If you're one of the few, the answer is simple: Get a different bike.
Given time/miles, I think you'll adjust, or find a solution that will work for you. Just hang in there... Best of luck.