1. You should be able to remove the lines from underneath with a regular wrench. I never used a crows foot on either line. The subframe was dropped for this.
I've done it w/o the subframe being dropped and was able to get to the top line on the rack by going though the engine bay over the trans and under the brake booster. I had the airbox out at the time so it may have afforded some space for my arm. Got about a 1/4 turn at a time and had to flip the wrench a lot but it worked. PITA vs. dropping the subframe.
2. Yes, in order to check the rack for leaks you have to remove the inner boots off the rack. The steel clamps will have to be cut to move the boots. If you find out that the rack is not leaking then make sure you put the boots back in place and use a heavy zip tie to keep it on the rack. This will ensure no dirt, etc. gets in there.
3. If the pinch welds are junk then I'd go with the inner rails and a piece of wood. You have to be able to support the weight of the car without using the rear of the subframe. When I changed out my rack I used 2x4's on a set of stands under the inner rails, then a set of jackstands under the front of the subframe. Put the jack under the rear of the frame and loosen the rear bolts until I could drop it the 3 inches or so that I needed to pull everything. Had another set of stands under the rear for it to rest on once I lowered it. I never trust a jack to hold anything.