But wont there be a slight variation in retention times from direct injection to SPME injection, or should I just use the direct injection RT's for SPME data?
I would expect differences in retention between SPME and liquid injections. How big the differences are will depend on the operating conditions. If there are differences in retention then the peak that you are calling MIB in the SPME run, which elutes at the same time as with the liquid injection, is not MIB.
You have still not posted the retention times of the MIB and geosmin peaks for your lowest standard; which produces larger peaks than the high standard so finding the peaks should not be a problem.
What are the retention times for a standard in water made up to 100 times as concentrated as your current highest standard ?
You also need to calculate how much of each analyte is in your lowest and highest standards.
Peter