Interesting... I have looked at Farstone's compatibility list and most Star Wars titles are on there, including K1 and TSL. This is a preferable method to the numerous and often shoddy No-CD cracks available out there, which are as we know, illegal and potentially dangerous to the system.
That said, is this what you are using to play your game, rjalbert32? Although Evil Q has reported difficulties with some systems in that section of the game due to the high number of NPC pedestrians, I would think also that using the actual game disc and not an emulator would give you the best results in a problem area.
I know you said that the game disc was clean, so I assume you are actually using a physical disc, but if not, that is one thing that I would change as a test condition.