There is one thing you can do as to parts you wish to remove but that are part of a mesh you want to keep: If possible, find out where they're mapped from on the texture map; if it's unique (or you're trying to remove all parts which are textured by that area) use the alpha layer to make them invisible. You can also do this with, for example, window openings: I've made long club car-style windows from regular coach windows by alpha-masking alternating pillars between them, and given a non-New Haven locomotive cab New Haven-styhle arched side windows by masking the area under the new arch. Be sure to use all-black (0,0,0) in your new masked-out regions of the alpha layer. This is also helpful for removing road numbers: substitute a set of alphanumerics that are completely masked out, or declare your model has no fonts and replace the required dummy font maps (which will then be used) with all-masked maps.
It's invisible paint, like an old Bugs Bunny(sm) cartoon... but you have to get lucky in how the creator mapped the items you want to paint with it.