This sounds as if there might've been a problem/incompatibility with the Lower City Cantina, tar_m03ae, wherein either the installer didn't add the 4th Vulkar/another mod overwrote the file that added the Vulkar and since that scene's scripts were modified to have the Vulkar move the game crashes as a result.
Can you add your tar_m03ae.mod file so I can download it and have a look myself? I might be able to fix it for you.
You now have total freedom to repair the airspeeder whenever you like, it will just be temporarily immobile for the duration of the Visquis and Goto story. When Visquis contacts you, someone will steal the power cells if they were installed, or rig the speeder to destroy the cells upon installation otherwise. You could wait until after completing the whole planet to start repairing the speeder if you like; the first time you install the power cells they will still be destroyed via sabotage, but if you picked up the extra cells on Goto's yacht then you can just immediately install the new ones. Thus you still have the opportunity to gain influence with both HK-47 and Mira. The "once again" message will appear only after the power cells are installed for the second time, though it just refers to whenever the speeder was usable last, whether that be under your care, or its previous owner's. It just acts as confirmation to the player that the game successfully registers the airspeeder as now in its final stage, one of permanent functionality.