I doubt that your hood pad is damaged...except cosmetically...replacement is up to you, and since you're already familiar with what goes on in the process you can choose to go ahead with it or not...only you know how your techs do work.
I can't imagine having such a large stain from such a small hole in the reservoir cap. If they did unscrew the cap, then the excess fluid would have just trickled out of the bottom of the cap, and not through the little hole. Still, they offered to replace the liner, and that should be consolation that they are trying to correct the situation.
As far as tools for DIY projects, there are only a few specialized tools you need (and I don't have them either). I would only buy the specialized ones whenever the need arose.
So far, I have gotten along with a moderate collection of metric wrenches, sockets, and ratchets. I just recently bought a small set of hex sockets when it came time to go after my alternator and belt tensioner, but my regular set of allen wrenches got me through most of the time.
I did buy a punch tool for doing the brake pads, since you need to hammer out a couple of pins in each caliper to remove the pads.
Should you ever decide to get really bold, then a torque wrench would be handy.
Again, most of the really exotic tools don't get used frequently, so don't worry about them. For DIY guys like me who are just now venturing past the engine oil dipstick, just buy tools as you need them.
Christmas is around the corner, so pass hints to loved ones about how you would really want the Husky or Craftsman 500,000 piece tool set!!!
Oh yeah, get a manual or CD specific to your model and year...sure clears up a lot of unknowns...