Joe,

Any sooting is likely to be evidence of a problem with the exhaust. I think your new pipe has cured that so you should be OK. I assume you have a blower to evacuate the housing of fumes during the start cycle. If not, that should be a part of what you are doing. The air intake for the box can be run through a large filter so both the generator box and the generator air intake are receiving clean(er) filtered air, further minimizing the soiling of that new white interior.