99 Mustang v6 3.8l misfire code #3 cylinder

Wish someone had some info on this. Got the same problem. 99' V6 that sat up for about a year that was given to me. I replaced a bad fuel pump, egr solenoid and valve. It ran great for a day but had an exhaust leak on the passenger side on the middle cat. Then I started getting a miss occasionally during low RPM cruising (ie 5th gear below 50mph) or sometimes during acceleration (ie shift to 3rd gear, accelerate, lose fire in the cylinder for 3-4 seconds). It's very intermittent. Comes and goes when it pleases. Initially, when it happened, I found that the plug wire on the #3 cylinder was cracked and arcing over to the EGR tube. I replaced all the plugs and wires and it did it less noticeably but it still occurred. Then I detached the battery cables just to reset some other codes that I had fixed and it cleared up for a whole day. Ran perfect. The next day however, it returned about 3 miles into my trip to work. Pulled the codes again and still getting the P0303, #3 cylinder misfire. The only thing that I know is wrong with it currently is the exhaust leak. Apparently, at some point the middle catalytic converter on the passenger side had to be replaced and rather than drop the exhaust and weld in the cat correctly, the shop just welded the bottom side of the joint. So the top half is just free flowing exhaust. I imagine this could be playing havoc with the 02 sensor on that side. Going to drop the exhaust and fix the weld tomorrow to see if it helps.