Can't clean a melted cat. If you are getting misfires you may screw up your new cat again! Unfortunately you can't afford to drive it much longer without possibly melting the front one again. Just get the rear one changed.
Unfortunately without actually testing the main rear or visually looking at it you won't know the condition it's in, but it does need attention ASAP.

Missfires Can Be Caused By a Million and One Things,

Vac Leaks
Wiring Issues
Spark Plugs(Even Fresh Spark Plugs That Are Crappy Quality.... E3 And Such)
Ignition Coils
Alternators (Search EMI)
MAFS
Injectors
Injector O-Rings
Intake Gaskets
TB Gaskets
PCV Hoses
PCV’s
Malfunctioning EGR
Malfunctioning CAS
O2 Sensors
Aftermarket Intakes
Intake Hoses
Vac Lines
Timing Chains
Timing Chain Tensioner
Broken Cam Gears
Malfunctioning Cam Sensors
Incorrect Crank Gears(The I4 Has Like 40 Different Configurations For Whatever Reason)
Incorrect PCM Flash
Issues Within The PCM
PCM Wiring
Bad Diaphram Within The FPR
Issues Within The Fuel Pump
Dirty Fuel Filter
Dirty Fuel Lines
Pre-Cats/Poor Exhaust Flow

I had a misfire, it was the poor exhaust flow, pre-cat causing it.

 

Well when I get out of my car, it smells like something is burning when I get out and stand by the front every time. Could it be burning oil? What causes this?

 

Could be the special coating burning off the new exhaust, this prevents it from rusting before you get it. It will start rusting after it burns off. Could be oil dripping on the exhaust.

 

Next time open the hood to see if there is any smoke coming up. Don't breath it in though.