1. Pretty sure the owners manual says 1 quart per 1000 miles is acceptable. The 5w40 should help
2. The car probably just needs a good tune up. Clean the MAF sensor,check the air filter,change the fuel filter and plugs. The boxer motors are naturally rough due to the unequal manifolds.
3. Get the lower shifter bushings .
4. Normal. Changing the fluid to a nice synthetic helps.
5. It's fine
Read the Uninombers Manifesto. Most of this stuff has been covered there.