Great suggestion, Brett.
The Inguz program will also let you play with room eq.
I am not aware of any software solutions from Logitech to the phase inversion of analog modded SB2 and 3.
The developers at Logitech have made great strides in their software and usability. While you might be able to get firmware 15 to work with 7.4, you will be crippling some of the features.
There are electrical ways to maintain correct phase. The easiest is to use an external DAC. The digital output of the SB is always in phase. I have yet to hear an external DAC that sounds as good as an analog modded SB with a good power supply, but if this phase issue is important to you, a external DAC may solver your problem.
If you are using a TT and SB combo, you can reverse the polarity on your speaker wires and also reverse the polarity of your phono cartridge wiring to come out with everything in phase.
Another option is to use a line level transformer. The transformer will isolate the + and - leads and you can reverse the output wire to maintain correct phase. You can get a step-up transformer to raise the voltage level of the modded SB. The drawback is that current is lost. You should use very short connecting cables.
A lot of tube pre-amps invert phase. I have a prototype tube analog section that increases gain, inverts phase and sounds very good. Unfortunately no chassis for it yet.