That exhaust pipe and muffler are both aftermarket, the actual header pipe is stock though... The Supertrapp's aren't really known for being a quiet exhaust and I doubt that you could bend those tabs back and get a seal of any sort. Everybody has different opinions on exhaust but if it was my bike I would look for another factory muffler, they're nice and quiet and usually pretty easy and inexpensive to source
You do need special tools for the doohickey replacement. A rotor holding wrench and a rotor puller. Eagle Mike can sell you a complete kit that has all the parts to do the swap. You could also borrow the tools from another KLRista if you can find someone in your area that has the tools and would be willing to borrow them out.
Stock fuel tank is steel. Lot's of guys bolt on IMS plastic tanks for added capacity and crash protection. If your steel tank is not all rusty inside and has no leaks it's just fine though.
As far as fluids, your manual will tell you what you should be using. Lol, and on oil everyone has their own preference!
I use Rotella T 15W40 in my bike. I buy it at WalMart in gallon jugs. Filters are cheap and I keep a few extra on hand. I'd also flush the brake fluid and rad, and give the brakes a good once over replacing pads if needed. Stopping is more important than going sometimes! Lol.
I'm also guessing that you'll need to go through the carb and give it a good cleaning, even more so if it sat with gas in it! The fuel degrades over time and builds up sludge's and varnish that plugs jets and such. Good time as well to check out your fuel lines and vacuum line to the petcock to make sure everything is in good shape with no cracks or deterioration.
You'll probably have to spring for some new tires as well once you get it running, especially if they are more than a few years old. Lot's of good suggestions on the forum here on tires, maybe even a few battles! Lol! I'd get it all put together and running good before I bother with the tires though.