2003 Yamaha YZF-R6 Installed baffle now idling weird/bad

Reposting my post from r/motorcycles to maybe get some help.

I bought this 2003 R6 in Oct of last year http://i.imgur.com/iT6Ndfv.jpg it came with a shorty muffler that didnt have the baffle installed in it. The bike was very loud, So loud in fact that on the highway through my helmet and wearing headphones it was impossible to hear anything else and would leave my ears ringing.

I found out for this muffler I needed a ring from the maker to install the baffle, Conctacted maker said they no longer make the rings for this type. Took the baffle I had that came with the bike (just not installed) and had a shop weld it inside my muffler where the ring would of held it in, now its just welded.

2 days after doing this my bike is idling very low on startup. It would usually get up to about 1900 rpm while warming up then sit perfectly at 1200 which is what the manual says it should be at. Now it idles around 1100 randomly bouncing to 900 while warming up and sometimes after driving for 20 - 30 minutes it will idle at 1900~ while in neutral. IF I turn the bike off and restart it will idle at the perfect 1200 for maybe 3 min then drop. Did I mess up my bike? How Can I Fix this. if you have any info it's greatly appreciated thank you!

Edit: Idk if it matters but in Jan of this year I had to get the cylinder head replaced. They replaced it with a used one off another bike like mine. It idled and ran perfectly until I did the weld.