Going to post this regardless of JuiceCBean having successfully fixed his issue:
I got tired of trying to figure out which color went to which pin on my cables because they were all different. So, I ended up just building the arduinoboy with a link port built in to the box. Made it much easier as there is reference material regarding the pin out on a link port. With it, I can hook up any old cable to the arduinoboy and even have the option of using a multi-link adapter(DMG-07, after being modded*) so I can hook up three DMGs to the one arduinoboy. Might be useful if you end up modding yours/making a new one in the future.

Edit: Now that I think about it. The reference I used for the link port was the one on the schematic for the arduinoboy.
This whole post, of course, isn't valid if you don't have a dead DMG or two. Seeing as how you can't just go pick up a link port from your local Radioshack.

*http://www.flickr.com/photos/lameboymusic/sets/72157607419956111/ - Credits to low-gain

Great news!  It turns out that I was indeed using internally connected two pin terminals, which was throwing EVERYTHING off!  I went to Radioshack today and picked up some new terminals that were NOT connected internally.  After hooking those terminals up and doing some resistance measuring to determine correct pin orientations, I was able to get output on a Gameboy Color using a microKorg keyboard and Trash80's mGB software!  YUSSSSSSSSS   Thanks everyone for being so helpful.  This really is an awesome community.  It turns out that my problems were caused by my n00b mistake of purchasing the wrong terminal blocks.

@nitro2k01, I am still interested in performing the pin swap mod on the DMG connecter on my cable.  I looked at the flickr photos you linked and they make sense.  I really just don't know what tools I would need to get the job done.  Any advice?

Quite possibly yes.

https://www.youtube.com/watch?v=uSvJaYxRoB4

It seems I have discovered a problem amidst all of this.  So I just looked up some specs on the two pin wire terminals I'm using.  It says "connections jumpered internally" and "pcb terminal block with internally bridged soldering metal."  Does this mean that the two pins on my terminal blocks are connected?  I got the hunch that this may be a problem while doing some resistance testing.  It turns out that I can connect the +5V to either of two pins on the same terminal and the LED's still light up.  So am I right about the terminal blocks?  I'd say I need some new ones. FUUUUUUUU

Terminology note: Twisted pair just means the wires are twisted around each other. This has nothing to do with whether the signals are crossed over. USB has twisted pair wiring for the signals because it helps the signal integrity. On a GB link cable, SIN and SOUT crossed over because in on one end becomes out on the other end. The two things are completely unrelated. Any one cable can do, none, one, or both of these things.

The wires are swapped on each end of the pins within the stock link cable assembly: This is so that the data coming from S-OUT on one game boy or accessory device is going into the S-IN of the other device, and vice versa.

Sorry, I must correct myself, they are not a twisted pair. I got things confused with USB for a second. My bad.
Nevertheless don't get confused with S-IN and S-OUT labeling. Precisely because they're not a twisted pair the pin that is S-IN on one side is naturally S-OUT on the other.

So you're saying that if I measure the resistance of the S-IN and S-OUT pins with the stripped side of the wire to find their corresponding wire colors, that I should switch the two around?

Not sure if this has been addressed here but make sure to take into account that serial in and out are a twisted pair, meaning the pin that is serial in on one side of the plug connects to a different pin on the other side. When I measured I used the cable plugged into the DMG and this wiki entry http://littlesounddj.wikia.com/wiki/PC_ … Interface.
I ended up with this:

which you could use to measure while having it plugged in to reverse engineer the wire color to pin mapping. just keep in mind that 2 and 3 are flipped on the other side.

If I do that Mod, will I still be able to power the Arduinoboy with the Gameboy?

Ok, then you should do the pin swap mod using the gnd pin. The shield is the metal thing that wraps around the wires inside the cable. It should be connected to the sleeve of the link port connector which in turn connects to ground inside the Gameboy. If your cable only has wires inside and no shield wrapped around the wires inside the cable, well then you're screwed.

You lost me at cable shield and connector shield.  Are you referring to certain pins?  I definitely need to use the SOUT pin.  I need all the pins necessary to use full midi in and out capabilities.

I'm sure you're right about that.  I'm a total noob when it comes to MIDI or gameboy mods.  All I know is that in Trash80's schematic, he connects all but one pin (pin 4 I believe) on the DMG cable.  I'm assuming that the clock is connected.  Please correct me if I'm wrong.

The trick is to use the cable shield as ground, since the connector shield is connected to ground inside the Gameboy. Alternatively, you could move and reuse the SOUT pin (the one  that sends data from the Gameboy) as +5V if you don't need that functionality (sending MIDI from the Gameboy.) Without some kind of ground connection, the circuit won't work.

I don't think CLK is the same thing as MIDI Clock in this situation, it's more the clock speed for synchronizing CPU cycles…