I used a Dremel with a cut-off wheel to shorten the struts. If you don't have one, a hacksaw will do just fine.
I had the same situation as you regarding the screws - used two of the short ones for the front fender, and one to attach the rear fender to the bike frame. I have a large collection small nuts and bolts (This is mandatory when you're retired, you're not allowed to retire unless you have a large collection of screws, nuts and bolts in your workshop!) You could always go to Home Depot and buy a couple of metric nuts and bolts to go through the holes for the struts on the rear dropouts.
Don't worry about the the rubber "accordian" brushing against the fender; it's a non-issue, and won't affect the safety of the bike in any way.
And, yeah, your local LBS would gladly take your money and install them for you, but don't wimp out, YOU CAN DO IT!
I don't know your age, soseono, but I can tell you that the whole time I was growing up, I was always told that I "wasn't good with my hands". I was your typical non-athletic bookworm fat nerd. After I got married, I got a job at General Motors, working on the line. That really opened my eyes as to how even very complex things like an automobile are assembled through a series of logical simple steps. Then I realized, "If a dummies like me can put these things together, then a dummy like me can work on it and fix it." I eventually went on to get an apprenticeship as an Industrial Maintenance Electrician, after working for 9 years on the line, and spent my last 24 years fixing anything and everything electrical that broke down. And many times it was something I'd never seen before; you just had to figure it out as you went along. Frustrating? Yes. Challenging? Yup. Satisfying? You betcha!
So I guess what I'm saying, is, don't be intimidated by technology or things mechanical. Dummies like you and me put them together, so dummies like you and me can figure out how to fix them or modify them to our liking. If you're taking something apart, use your digital camera to take pics every step of the way. Lay out the parts in a straight line, in the order you take them off, and just reverse the order when you put them back. There's hundreds of little "tricks" pros and tradesmen use every day. You can learn them and apply them too, no matter what kind of Do-It-Yourself job you tackle.
So I repeat. "Yeah, your local LBS would gladly take your money and install them for you, but don't wimp out, YOU CAN DO IT! "