One of the issues with index shifting is all the drivetrain parts need to be designed to work together, Even getting a different bottom bracket or crank, won't solve the issue of the chainline for the cassette now being off; does the bike 135mm dropouts? Regardless, I would get the proper front derailleur or there will always be some problem with shifitng. As far as the SQ crank goes, at some point within the first 10-20 miles you should re-check the torque. It's rare that it will loosen up, but if it does and the result is a damaged beyond use crank. So, either get yourself a torque wrench, or give a really good effort with a 8mm socket and 8" socket wrench..