That is normal.

All LEDs light up. Mode select button functions and light up with each press. DMG set to master and Arduinoboy set to master when I press start LEDs cycle in time with bpm.

Edit: spelling

No, probably not normal. Can you do what I suggested above with regard to that? Please check during the startup sequence that it cycles through every LED and that none are missing from the sequence. Then also press the mode button and see if that does anything.

Ok. That seemed to work. Arduinoboy powers on when I turn on game boy.  Cycles through LEDs. Once the cycle completes they all turn off. Is that normal?

Correct, that's the 5V which is normally unconnected if you're using external power.

Also the picture of the link connector can be kind of confusing it's showing the link connector as seen on the Gameboy, which would mean that the connector would be mirrored if you looked at the plug. BUT that image is incorrect and you have to pretend that you're looking at the actual plug on the cable instead.

I'll give it a shot but I'd like to point out that on the pic on kitsch's site one of the outermost pins on the DIN is empty.

Try this. Just to confirm, this assumes in both cases looking at the connector from the front.

The changes from the pictured wiring, in words:
On the link connector:
* Move the green pin back on the connector back to where it was originally.
* Move the red pin to where you just removed the green pin from.

On the DIN5 connector:
* Move the blue wire to the outermost pin, opposite side of where the red one is.
* Move the green wire to where you just moved the blue wire from.

Assuming I didn't mess up, that should work.

This how I have it wired. This is looking at the male end of the plugs. I moved the green wire from top right to top left.

Can you tell me exactly which pin on the plug you swapped from and to where? And also where on the board you connected that wire?

As for the status LEDs. They should do a blink sequence for testing on startup, then light up only one LED (when idle) indicating the mode. Carefully check if any of the LEDs never light up during the startup sequence. It's possible you connected one LED reverse or otherwise incorrectly and that that LED happens to be the active mode. You should also be able to get around this by trying to press the button to switch modes and see if any LED lights up. Something else could be wrong but start with that.

As it is now the Arduinoboy will only power up using external power so I assume the 5v pin swap was done incorrectly. What about the status leds not lighting up beyond power up?

That mod is only necessarily if you want to power the Arduinoboy through the link cable instead of using external power. Choose one or the other. Also, you need a ground connection over the link cable. If you used the ground pin for the pin swap, you need to connect ground through the shielding of the cable. If you used the data out pin, this is not a problem but then of course you're losing the MIDI out capability.

As it is now, you're backfeeding power into the Arduinoboy through the data pins of the link port, which is what is making the backlight light up dimly. This would happen regardless of the pin swap, though.

Okay so I bought the Xiwi  Arduinoboy from kitsch and modded a DMG-04 Cable. When I plug the Arduinoboy in all leds flash then nothing. No other leds light up beyond the power up. I did the trash 80 pin swap to get the 5v. Was that necessary? Also the backlight on the Dmg lights up even when off. I'm sure there's is more info everyone will need to answer these questions but I didn't want to give out useless info. Yes, I used the search function but there's so much buried in these forums it might be faster just to ask again. Please and thank you.