I found the mapping for joyport 2 after 30 minutes of guess and checking. :) I will be making an adapter for this soon and post it on my web site but I have it jerry-rigged right now. I have the full mapping of joyport 2 with the data 2 and 3 wires. This was tested with the light gun and duck hunt so it works great! If anyone could e-mail me a working copy of Arkanoid in PC Jr. format(Standard QND doesn't work) i'll try to get the Arkanoid controller going. Enjoy!

Joyport 1
-------------------------------------------------
Looking at front of Dr. PC JR:

01 02 03 04 05 06 07 08
09 10 11 12 13 14 15

Looking at end of NES controller:

1
2 3
4 5
6 7

Based on this mapping, here is what I did:

PC JR<---------->NES

01--------------1
12--------------5
13--------------7
14--------------3
15--------------2


Joyport 2
-------------------------------------------------
Looking at front of Dr. PC JR:

01 02 03 04 05 06 07 08
09 10 11 12 13 14 15

Looking at end of NES controller:

1
2 3
4 5
6 7

Based on this mapping, here is what I did:

PC JR<---------->NES

01--------------1
15--------------2
09--------------3
05--------------4
12--------------5
04--------------6
07--------------7