Ari, I sympathize with you. You have to tackle every problem systematically. Start with the film backs. Make certain they are always clean and free of dirt. Check the dark slides for any dirt or sharp burrs that could cause the scratches. Are the scratches in a consistent direction or are they randomly oriented? What direction do they go? This might help clue you in to the cause of the scratches.
Water, while it may be desireable to use distilled water for every facet of development it is not terribly practical. I use distilled water for developer and for the presoak as well as for the wetting agent. For the rest of your water usage you need to filter the water using a 2- 5 micron filter. Do not use a carbon (charcoal) filter, or a Britta type filter as they can often leave small bits of carbon media in the water. You may also have to look into the addition of a water softener in your water system. In my system the water goes through a 2 micron filter, then a 2 micron carbon filter ( removes chlorine) , then water softener, and then at the point of the darkroom sink another 5 micron water filter (non carbon).
Overly strong stop bath can cause tiny "explosions" in the emulsion when it contacts developer. I use a water rinse, then slightly weak stop bath, then another water rinse between developer and fix. And to be certain that my rapid fix does not die in the middle of a film run, or leaves any particulates in the tank or on the film, I always use a 2 bath fixer. That is the first 3 minutes of the rapid fixer fixing is done with container A, and the last two minutes of fixing is done with container B. When container A comes up exhausted during a fixing, I extend the time that the film is in Fix B. Then fix B gets poured into the Fix A bottle and becomes the new first fixer. I then mix brand new fixer for container B. This way I can always check to see if the fixer is exhausted during a film run, and fresh, barely used fixer always finishes up the fixing process and helps to dissolve any particulate that might be floating in the first fixer.
After washing in the highly filtered, softened water, I then use photo flo made with distilled water, although at a far weaker dilution than kodak suggests. I also add a touch of 91 percent Isopropyl alcohol to the wetting agent. I find that it speeds drying slightly. I then, squeegee the film, yes that's right, squeegee the film using a Jobo Squeegee which is wet with the same diluted wetting agent on it. I would not use the squeegee dry. The film is then hung in the darkroom over a sink. I keep the squeegee meticulously clean and in it's original packaging. Do not let wetting agent dry on the aqueegee. The rationale for the squeegee is to speed drying, prevent water marks and to physically remove any small particles that may cling to the film and ultimately dry into the emulsion. So far this system has yielded me very clean negs.