Ron,
I don't know where you live, but the problems you're having now are common to us all. You've put a fair amount of miles on the bike in a short time and that makes you more likely for close calls just by the odds alone.
Close calls go with riding bikes, but it might be that it seems worse than it really is? I was really scared just to be on a $40k bike for a while, and that still gets me from time to time. Plus, I KNOW I drive this CVO harder than I have any other bike, and that can make for close calls too.
5 years ago I lost my wife when we hit a deer on our '07 Electra Glide. I was scared to death to ride after that, but something inside kept nagging at me to keep going. The fears were in my head, and mostly not real. Oh sure, the threat was still there. It always will be. It's just that I turned that threat into something that was waiting for me every tenth of a mile there for a while. I'm not saying we should drive like there are no real threats out there, because there are, and that never means you should be careless. What it means to me is that you know the risks and accept them because you love the sport, or you have to get out of it entirely. I couldn't do that. My wife loved to ride and knew how much it meant to me, and she would have been heartbroken to know I quit because of that accident. Conversely, she would have been so proud of me for fighting back my fears and riding on.
Different situation, I know, but it sounds like you love to ride and may be going thru a similar crisis of mind, so to speak, so I thought I'd share part of my story with you.
As to the subject of the bike, it sounds like you still need to 'make it yours'. Little things like footboard extenders, different foot brake lever, roll the handlebars a bit. Adjust the handlebar controls and the angle of the levers. Maybe get a new windshield. Things to help you ergonomically. Take your seat off and adjust your backrest. Whatever it takes. You've bought an awesome machine, and it's just waiting to be the love of your life, brother.
As far as cagers go..they don't look and even when they do, they don't see you. So add some driving lights up front. Add a brakelight modulator in the back. Change your front turn signals to daytime running lights. Drive with your high beam on during the day. Make yourself as visible and differentiated as possible. Drive slower when the risk is higher. And above all...drive like you're invisible.
I hope there's something in here that will help you, Ron. I'd hate to see you quit riding, but in the end, only you can decide what's best for you.