The most important difference is that it has a primary mirror 3 times the size of the Kuiper Airborne Observatory.
Which was about as big a telescope as could be fit in a C-141. Being the C-141 prototype, there were enough idiosyncracies in its configuration to make it not worthwhile to convert to the stretched C-141B configuration. It was one of just a handful of surviving C-141A's to not be converted back in the late 1970's early 1980's.