If you mix the cotol 240 properly and thoroughly into the Aquaseal it should not harm the suit material. I do not use it as a cleaner however as it is overkill and the stuff is potentially nasty to some materials when it is full strength.
Clean is also relative. Remove any skin oils and (if you ever used them, don't ever use them again as they are very persistent and hard to remove) any silicone / armor-all sprays as they will interfere with adhesion. I tend to prefer soap and water and perhaps some rubbing alcohol for degreasing and stay away from harsher potentially suit eating chemicals.
I have never noted any shortening of patch life with accellerated Aquaseal. I have a BC somewhere that had a pin hole patched with aquaseal in 1987 and the patch will be there long after the BC turns to dust. Accellerated Aquaeal is slightly les flexible, so ifyou are coating a large area (knee pad, etc) then the slow cure is worth the wait - otherwise, add cotol 240 and get it over with in 2 hours rather than 24.
Ditto the suggestion to patch the inside of the suit. It looks nicer and subjects the patch to less wear and tear.