What do I do to fix this problem or do I have to put my factory exhaust back on?

Hello, I honestly do not know of a direct correlation between exhaust flow changing and an engine misfire starting. Cylinder 5 misfire would typically start due to a spark plug, coil, fuel injector or valve train issue. Or, base engine issue. I can't really imagine a direct result from changing exhaust. It could be that freer flowing exhaust has stimulated a concern to become more apparent? Too hard to know. Although I suggest that "factory" equipment eliminates variables when you have a problem, I would also say in this case that it would be better to troubleshoot and see if you can drill down to the misfire that is being recognized before doing anything else. If you want some help, seek the guidance of a local shop near you. https://repairpal.com/auto-repair-near-me Click the link or call us at 877-913-1554. We'll gladly find you a certified RepairPal shop in your area.