Replaced starter less than 20,000 miles ago...Also when warming very rough. Had this problem before went away after replaced starter now is back

I replaced the fuel pump, but it runs like crap now. The relay, and fuses r fine. It spits and sputters, and won't accelerate at all. I don't have a lot of cash to sink into it, so hopefully I can get a idea of what's wrong with help from someone here

After it rains, about every 3-4 days where I live, I have about 2-3 inches of nasty standing water in the middle of my trunk! I have checked the seal around the trunk opening and it is in excellent shape, no tears or cracking. There are also no rust spots or holes in the body around and under the rubber! The water is filling in the middle area where the spare tire goes. Its not wet on the insides of the trunk on either side, the water us getting in how?

Driver's side electric window will not go down all the way,
How do we fix this problem?