How do I hook the joysticks, Select and Reset and difficulty switches back up?

Having working switches and joysticks is probably a good idea!

And since you'll probably chop up sections of the board that contain the original ports, you'll need a way to hook them back up!

No matter how much of the board you're going to try to hack off, the best place to get the hook-ups for those things is off the RIOT chip...

   (The other chips have been removed for clarity)

Here's the RIOT chip. It handles the I/O functions of an Atari 2600, and it's topmost chip on the board (of any model 2600). This is where you hook up everything but Trigger 1 and Trigger 2. The triggers go to the Stella chip for some reason I can't comprehend. But, whatever.

Looking at the RIOT chip from above, here is where to hook up the controls. There's 40 pins on the thing, count them out this was on your chip to find the numbers!

1: N/A
2-7: Cartridge access lines (don't worry about them)
8-11: Joystick 2 UP DOWN LEFT RIGHT (respectively) 
12-15: Joystick 1 UP DOWN LEFT RIGHT (respectively) 
16: Difficulty switch B
17: Difficulty switch A.
18: Beats me!
19: Who knows?
20: (Shrugs)

21: Black or White switch (snicker! how useful...)
22: ????
23: Select switch
24: Reset switch
25-40: Stuff you don't need (mostly cartridge access crap)

Switches are pretty easy to hook up. I'm leaving it up to you where to put them, but I'll tell you how to hook them up. First, make sure they are run-of-the-mill ON/OFF switches. Pushbutton switches of this type are normally called SPST switches. (Single pole single terminal if memory serves) Slide switches that would be good for the Difficulty switches are called SPDT. (Radio Shack part #275-409A). Single pole DOUBLE terminal. They have 3 connectors on the bottom, the common terminal is the center, and the other wire would hook up to either the left or right terminal, depending on which direction on the switch you want "ON" to be.

Here's a really sloppy diagram of how to wire a joystick. The RED BLOBS indicate the UP DOWN LEFT RIGHT switches that you will use. Notice how there is a GROUND in the middle, that leads to the G spot on the left. You can see how the wires from the switches lead to the appropriate spots on the Riot Chip. (hence the R in front of the numbers).

The BLUE BLOB (wasn't that on MST3K once?) is the trigger. It also has one connection going to GROUND, and the other one goes to pin 36 of the Stella Chip. (The trigger may cause problems if you cut off too much of the board, but I will cover that later).

The YELLOW BLOBS are the Difficulty A & B switches. Again, they both go to GROUND, and the other side goes to the proper pins on the Riot chip.

Regarding the Trigger, to find Pins 36 and 37 (Triggers on joysticks 1 & 2) on the Stella chip, the pin numbers are in the same positions they were on the RIOT chip since they both have 40 pins. As you probably recall from the 'Getting Video" sections, the Stella chip is at the bottom of the board. 

The only thing to watch out for is that the Stella chip is upside-down on the Atari 2600 Junior board. If you look up at the Stella picture there, you'll notice a little half-moon and a dot on the left side. On all chips the dot indicates where Pin 1 is. So, keep that in mind when attaching a trigger to the 2600 Junior. Or when doing anything else!

Another note on the Trigger: Removing certain resistors will cause the trigger to be stuck on. (reference: making of Vagabond). If this happens (and it WILL if you saw enough off the board) do this:

Putting this simple circuit of 2 resistors between the trigger switch and the connection on the Stella chip will solve the trigger stuck on problem. You'll have to do this for joysticks 1 AND 2, of course, separately. For non-schematic people, the wavy lines are resistors and the arrows pointing down are ground. You'll notice a metal stripe running all over the place on the Atari circuit board. It's also what the RF shield hooked up to, remember removing that? Well, that's ground.

Re-wiring the joystick is pretty easy, it's just that trigger thing might give you a problem. Although that problem won't arise until you start chopping the board up.

I hope this has provided enough information to allow you to hook up controllers! Good Luck!