Along the same lines... If i buy a NAND-X, besides the one cable I mentioned above, will the rest of my JR Programmer V2 cables work with the NAND-X?
I believe so, yes. I own both a NAND-X and JR Programmer V2, however you really only need a JR Programmer V2. My NAND-X was purchased used and came with no cables, so I always use my JRPv2 cables when using either one.
If you want a cable that you can program a glitch chip with, I don't think they make them. Regardless, I was able to repurpose a CK3 to NAND-X Update cable for this job. Simply cut off the DVD power end of the cable, then you're left with something compatible with the top right connector of the JR Programmer V2. From here you can either solder on a six pin female header (like the one in your first post) or solder directly to your glitch chip.
EDIT: This custom cable of mine is exactly how I solved the problem you describe. I got my JRPv2 in a bundle with CR3 PRO Full Post. Unbelievably, this cable was not included in my bundle... They really should have sold them separately.
Also, I almost never use my NAND-X anymore. JRPv2 is a perfect replacement aside from the fact that it doesn't have a case. This is another thing I wish TX did differently. If you're crafty enough, you can still construct your own case (which I eventually ended up doing).
EDIT2: I recall that the "smaller white connector" is a six pin Micro JST connector. Again, CK3 to NAND-X cable has one on it and can be purchased for cheap.