I am not sure if 3 hours are enough... While Immigration and Customs checks are ultra effective in TPE (dear Thai Immigration - do you hear this
), there is no pedestrian walkway to the museum - you will probably have to take (not-that-frequent shuttle) to Novotel and walk from there.
Immigrations and Customs are always hella slow when I go through TPE (they have, like 6-8 counters to process BR and CI's nearly simultaneous LAX and SFO flights, in addition to whatever else lands at 0600 for whatever reason).