Typically, using too many intersecting objects is a problem during conversion rather than in-game. Unless it's used very carefully, it becomes a really messy way to model. This is ESPECIALLY true if all those blisters are separate objects in TS, because from there they either have to be converted into separate submodels (ie, subsystems) in FS2 or they are merged into one object by PCS during conversion, depending on whether lights were glued to them or not.
Having PCS do a lot of that kind of merging is very dangerous for model stability. As WeatherOp suggests, it'd be a very good idea to spend some time just shooting and ramming the thing all over - especially at sections with weird geometry such as polygon intersections and stuff.
Oh and finally, the intersecting bumps mean you won't be able to get good smoothing at the parts where the blisters meet the hull, so don't bother trying.
