Aussie,

Do the fuel line first. IMO, I think leaving the tubes open if at all possible is the best thing. The engine, like any engine needs to breath. By that I mean, fre flowing air into the carb, free flowing exhaust out the muffler. Anytime you restrict the exhaust flow you do build backpressure but you can have too much which will cause the engine to suffer.

Back in the time where I was a part of building race engines for drag cars, the more quickly we could get the exhaust out (polishing the exhaust ports) and the more we could get the intake mixure atomized (cutting deeper ridges into the intake manifold plenums), the more power the engine made. We would do large displacement engines for street cars, run them with open headers at the track and turn some quick times, them we would add a muffler, even a straight through one and do the run again and loose a second or two because of the exhaust restriction.

What it boils down do, an engine is an engine in regards to it's exhaust flow, even 2 stroke versus four stroke. Restrict the flow, lose power.