No I do not believe it wil have a negative affect on the digital signal and if there were any affect I suspect it would be so minimal that you would not be able to detect it. I have used extension cables in such applications and even when transferring data on hard drives and have not encountered any issues. Good luck.
Although I have not used the Samson Go Mic in this specific application, I see no reason why it would not work. The mic is quite sensitive and should have no difficulty picking up the instrument. I imagine it will be necessary to try a few different settings to find the one that works the best. I use this Mic on a Mac, but suspect the drivers for Windows will not influence the behavior of the Mic.
I don't know what a software PC tuner is. I had purchased it to use with Windows at ease dictation, and it didn't do very well.. I ended up purchasing 2 other mics, and Dragon before I finally got something right...
I think the USB cable that comes with the mic is at least 12 to 16 inches; however, I have not used it because I use a very short cable to plug the mic into my Apple keyboard. You should not have any problem with an extension cable. There is a limit to the length for USB cables, but six feet is well within that spec. Although I would be sure to keep cell phones and so forth away from the cable and mic if you are doing any recording since these things can be affected by these devices.