I have used both JB Weld and Devcon inside of crankcases, and neither one has ever failed me. Lots of people mix these chemicals with aluminum chips, and I haven't even done that and still haven't had a problem. Aluminum powder or chips would make it thicker though, and easier to apply. If some epoxy in the right places can improve flow, then why not use it? Like waxhead, I also media blast my carters to provide better texture, thus better flow.
Over the years in 2 stroke evolution, many different practices and theories have been put into place. That's one thing that makes a tuner unique. Everyone has an individual style, skill, theory and reputation. It seems like no matter what, you're going to find someone that disagrees with you. Rick at Macdizzy has built a BUNCH of high-end race winning engines in quads. People spent so much time arguing that he wasn't doing things the right way that it got old for him to keep defending his own actions to people visiting his own website. His engines are still winning races, which is more than a lot of the other guys can say. Some of his writings are different from the 2 stroke "Tomes" (Bell, Jennings, Blair, etc) but his methods work, and his engines kick ass.
I realize that the largest gain in engine tuning is with the transfer and exhaust ports. If I take all the time to tune my carters and transfer tunnels to flow the way I feel they should, and my engine doesn't perform much differently than it would have without, not all is lost. It's part of being an enthusiast and a tuner to try different things and have different views.
I also believe that a well tuned engine with a proper exhaust can cause the reeds to open before the transfers are closed. I think this would be more on engines with very high primary compression. Perhaps the second reed opening is rare (How would I know?) but I don't think it's impossible. Wouldn't it be nice if we could have a way to see everything that happened in the engine when it was running?
WDJ, with all the above put aside, if I were buliding a MHR Team 2 engine, I would probably opt for some more aggressive carter tuning like is shown in the picture I posted. Over time, with enough opinions, you will hear many contradicting opinions and views. Some people think cartertuning is a waste, some don't. I guess it comes down to what makes the best sense to you, and what you feel will be a job well done!
Whatever way you choose to proceed, I sincerely wish you the best of luck in your engine build. You've chosen a fine cylinder!
All the best,
~Josh