I recently converted a 45 cc, the old one so I did not have the carb mounting problems you are having, however I would strongly recommend that you not break of the fins with pliers. If you send the flywheel to Peter at Whacker Engines he will machine it for your and balance it for $12 bucks. Send the thing down to him with your order and he will ship it all back together. The first engine I did I machined it down on a friends lathe, however $12 was such a deal that I just sent the next one to Peter to do. If you screw up the flywheel you will end up paying about half of what you bought the saw for to get a new one.
In regards to your muffler question, give Peter a call at Wacker, he is very helpful and I am sure he would modify the muffler to meet your needs. The other thing that you may find helpful is getting a Dynatron High tork starter to turn the thing over. You need to get the fly wheel turning fast enough to get a hot enough spark. Some are better than others, but mine needed the extra torque. I have since then started it by hand, but it is a pain in the neck.
Best of luck with your project.