Hey Jazzyvee,
Great to hear it fired up and seems to be doing what it was built to do. A note on that 1/4" input mod: following the wires in the photo, I believe that is a stereo jack. Meaning with an older model Alembic bass or guitar with battery operated stereo 1/4" output, a stereo 1/4" cable would allow you to plug straight in - without powering up the IN-2 - and the signal routing would be intact. Make sense?
And just to mess with you more, it could also serve as an OUTPUT of an instrument plugged into the 5-pin connector. HA!
I still believe that the "crack" you are describing is because you are overdriving something in the chain. Remember, your instrument can have almost a line-level output (enough to directly drive a power amp), then the F-2B is another preamp with a ton of gain, and then the SF2 is yet another. Try that setup you've described but turn the instrument's master volume down to about 1/2 and see what kind of volume / tone / noise you get using the other pres for gain. Remember that turning down our master volumes does not change the tone. It could be something as easy as that.
As for routing... IN-2 outputs are front and back, SF2 has inputs and outputs on the rear panel, but the F-2B is front in and rear out only. If you don't have an open slot in your rack which you could pass short cables through, this is where MODIFYING the IN-2 gets interesting. You will not likely need double sets of outputs on the front and the rear of the IN-2. So one set of those 1/4" jacks could easily be wired as a passthrough from back to front if you needed that. Furthermore, depending on what kind of signal you want to make available to the DI outputs, things can be wired accordingly with linked 1/4" DI inputs, mono summing resistors, etc. It's kind of endless!
I'll leave it there and let you think about all that. Sorry I get all nerdy when talking about this stuff. HA!
Jimmy J