I just though I would post this. It is originally from the vwvortex. It isnt my writeup, but it has useful pics and wording. The article and pictures are using the obsolete VB921, but the pinout is the same as the Bosch BIP 373. The first writeup works, but isn't the way the MegaManaul lists. For the MegaManual version, look farther down.
"Alright guys, I just got my 16v fired up using my v3 board to control spark. Im gonna try to make this a very detailed write up covering the whole process. Before I go on any further id like to say thanks to Dave (cdndub) and Calvin (kalvinlk) for all the help. This write up is based off of Dave's original write up but it will include a couple of things that were left out along with pictures. Thanks again guys.
First off, I purchased my v3 board already assembled because I didn't have the time to build it myself. Because of this I was kinda left out on the basic internals of ms. I read and asked a bunch of questions and eventually understood everything (well mostly everything ).
This pictures is good to use to get a basic idea of where things are located on the v3 board.
With all that said I will now get on to the procedures that need to be made to make this thing control spark.
First things first. TACHSELECT should be jumperd to OPTOIN. If its not please do so.
2. After that you will need to solder a jumper wire to the previous jumper and run it over to the +5 pad above the proto area. You can see the +5 pad on the top side of the pcb. Like Dave said, This will give you 5v to power the hall. (cleaner signal)
3. Next you will have to cut the jumper between XG1 and XG2 if there is already one installed. After that you will need to run a jumper wire from XG1 and IAC-1A. This is the input for the tach signal from the dizzy.
4. If not already done you will have to jumper TSEL to OPTOOUT.
5. This step pretty much depends on which firmware you are running on your v3 board. Basically this step is where you send a signal to the IGBT (onboard ignition driver) to let it know when to fire. On the v3 board the input is labeled IGBTIN. The output to this is what varies depending on what code you are using. The default output for the standard ms2 code is JS10 (ign). If you are using the standard ms2 code then run a jumper from IGBTIN to JS10.
I on the other hand am still using the ms1 processor but running it with MSnS -E so I can control spark. If your running MSnS like I am then the default output is one of the led's. In this case you will have to run a jumper from IGBTIN to the top of R26 with a 330ohm 1/4 watt resister inline. You will be able to see R26 from the top of the pcb board. You can also refer to the pcb picture posted above. The reason you don't want to use JS10 with MSnS is because JS10 is a input for knock control. Check out the pictures below.
6. Next jumper IGBTOUT to IGN if not already jumperd. This is the output to the coil (pulsed ground).
Now that all the internal mods have been performed we will move onto the wiring. Your basic hall sensor will have three wires. The three wires consist of a ground, power and signal. In almost all cases the middle wire is the signal wire. This wire will be ran to pin 25 or pin S1 on the relay board.
Next is the ground wire. This wire will most likely be brown/white or just brown. You want to find a good grounding point for this wire. The last of the hall wires is the power wire. This wire should be red/black. The power wire will be ran to pin 24 or the TACH pin on the relay board. Finally its time for the coil wire.
All you need to do is run a wire from pin 36 or S5 (relay board) to the negative side of the coil. This wire is a pulsed ground and will tell your coil when to fire. That's pretty much it guys. You've just moded your v3 board to control spark. If anyone wants to add to this or ask any questions please feel free."

For those that are using the V2.2 board, use these pictures to help you mod it for direct coil control:


The way it should be done according the the Manual:
The Hall mod should be done like this, but it will also work the above way.
Board Wiring:
Jump TSEL to OPTOOUT
Run a wire from TachSelect to XG1
Remove R12, Fit a 470R resistor in its place
Remove C30 and solder a wire from the top hole of the C30 position to +5V on the proto area.

Hall Plug Pinout:
1- Ground (ground should be a brown coded wire)
2- Signal (middle pin)
3- Power Supply Input
Megasquirt DB37 Connector Pinout:
24- Hall signal input (middle pin on hall sensor plug)
26- Hall sensor +5V source (Also TPS +5V source. Will need ran to both TPS and Hall sensor)
7- Hall sensor ground
Run the Hall signal output to pin 24 on the MS DB37 connector. Supply +5V to the hall sensor by running a wire from pin 26 (which is also the TPS +5V) to the hall sensor plug power wire. Run the hall sensor ground wire to pin 7 of the Megasquirt DB37 plug.