Question about muffler compatibility/back pressure!

So I’ve pretty much rebuilt my 06 recon 250 engine and got the timing dead on, not bad for a rookie. When I bought it, the original muffler had been hollowed out. After the rebuild I put that same crappy muffler back on it and it ran great but it was pretty loud. The seller gave me another muffler with it but it wasn’t for the recon, though it is a honda muffler. The pipe is bigger and shaped different but the muffler itself is the same shape and size. I managed to fabricate new mounts for it, cut and mended the 2 different size pipes together and installed the better looking, quieter muffler. Problem: The engine didn’t run the same. Stalled out as soon as it started. Even after somewhat warming up and a little tweaking of the idle screw it still seemed to struggle to stay running. Is it possible that there’s too much back pressure with the newer muffler or do I just need to make some adjustments? It’s obviously from a bigger engine hence the bigger pipe. I’m a bit apprehensive about keeping it running out of fear of damaging the newly rebuilt engine. Any advice is greatly appreciated!!!