I've been following this thread for a while and wanted to share my experience with lowering my bike. By the time I got my bike, the J&P cycles rear shock was no longer available and frankly, jerry-rigging a shock with a bunch of washers to make it fit really didn't sound like a great set-up to me. Fortunately, lowering links from T-Rex Racing just became available and based on a couple of other reviews here, I took the plunge. I'm very happy with my decision and I enjoy riding so much more now.
Although I had learned to one-foot the bike, having only minimal control of the bike at stops was starting to cause me so much anxiety that I just wasn't taking the bike out anymore. I was up on my tiptoes and walking or backing up on the bike was just out of the question. However, I read so much negative commentary on lowering the bike that I kept thinking, "I should just learn to be a better rider!" "I'll mess up the bike!" "I should just forget about track days if I'm going to lower it." So I put it off. I lost so much time actually enjoying my bike because of my fear of it. When I finally took it in to have the bike professionally lowered, my mechanic told me, "Don't worry about lowering it. You have to be comfortable on your bike."
So, just a note to naysayers of lowering: if you're a taller rider, you don't have to deal with those issues so quit with the judgment. If you're a shorter rider who is comfortable on a tall bike, don't shame other riders who don't have your level of confidence. Short newbies like me: Do your research. There are pros and cons, but the cons may not be that bad. You should enjoy your bike.
Besides...... lowering it isn't permanent. I first tried the J&P shock and for me it was just TOO low. Put the stock shock back in and kept riding. Ordered the T-Rex links and installed when I found the time. It's like the happy medium.