Is it my transmission?

I reciently jumped a curb and cracked the bottom (most forward)of my automatic transmision case. I have successfully stoped the leak using JB weld. The issue is, when I have the car in any foward gear; drive, 3rd, and 2nd. It runs/drives very rough. It shifts gears normally and my car runs fine in reverse. I believe I put the wrong transmission fluid in it. My reseach says I should have used Dexron III (replaced IIE), I put in 3.5 quarts of Dexron VI in it. I have also crushed in the bottom of my flex pipe on the exhaust(not sure how detromental that is). I dont know if I have damaged the transmission internally or if my flex pipe is the issue or wrong fluid type. I would like to note; sometimes when I check the fluid level, it reads none on the dipstick, then a few minutes later, its good. Thank you.