RE: Will this engine set-up cause problems?
A few more problems you may encounter are:
1) With the muffler like that, you will get a lot of fuel residue on the plane that will make for a messy clean-up
2) With the needle valve facing down, if you have a crash, even a minor one, you might easily break it off and have to replace the whole carb or at least the whole needle valve housing.
If it were me, I'd fix it now before it's covered. It's a big fix, but not really too bad.