Well, I can honestly say I had none of these problems
That being said, riding has never come
easily for me. Some people take to it instantly and it was never that way for me. I am an accomplished and competent rider. But I work at that and it wasn't an easy peasy road.
I chose a bike that was somewhat heavier (although not a pig by any means). It was a good deal and it worked out.
I was fine during MSF and took my time practising.
I'm 5'6" so I've never had a bike lowered and never will likely.
My one downfall is moving bikes around in an "engine off" situation. I basically suck at this and always have. A friend forced me to practice with my first bike but it's never gotten any easier.
I've recently made some gains in that department just out of necessity from being at the track and moving the bike around a lot. But I'll never find it "comfortable" the way other people seem to.