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I'd get a rubber upper shock mount. It would be softer and give a little more when you bottom out. Try a local parts store or Ebay. You could also get the front bump stops for a HHR. They are about $8. I haven't tried them but the pics look like a longer version of the stock C5 bump stop (which you could also use if you have your old shocks). They are likely too long so just cut them to the size you want, likely about 1".
Here's a pic, but the sponsor here like Parts Taxi or GM Parts House have them cheaper.
You can just throw the covers away. It doesn't look like you drive the car in crappy weather. Besides, millions of cars are on the road without any shock boots and they do just fine.
The car is pretty low. I do have the bushings cut in the front. When I jacked the car up, I was fully preparing to raise it back up some as well as searching for the suspension noise. IIRC, from floor to fender in the front measures ~25-25 1/2 inches.
As mentioned in a previous post, I lowered my car, yet retained the stock bolts. I had to be somewhat careful, though, as I have the F45 suspension set up in my car. Even after lowering, I'm at 26.5", ground to top of fender opening, at the front of the car...