MSD:

As a side note, I do not recommend using an msd. The stock ignition works fine if its in good working order. Just buy a USDM external coil distributor and plug it into the accords external coil. That would have saved me a great deal of time and energy.

External coil cars (swapped in a USDM distributor)
Cut off the plug to the stock coil and solder together the yellow/black and yellow wires together. They're really thick so trying to solder them together you need a friggin torch. Solder the small red wire from the MSD to these two. Solder the green wire to the small white wire from the MSD (the one next to the red wire). If you don't want to hardwire the MSD box on the car use weather pack connections and solder them.

Internal coil (JDM internal coil distributor)
Take the coil out of the JDM distributor and solder extension wires to the two wires that went to the internal coil. these things are tiny and doing the job right takes some fine motor skills. File a slot for the wires to come out of on the distributor cap. Solder the positive wire to the small red wire on the MSD unit, and the negative to the small white wire. 

If using stock ignition:

External coil: cut off the plug going to the coil, solder the yellow/black and yellow wires together. Tape off the green wire. Or buy an external coil USDM distributor and use the coil from your Accord.

Internal coil: just plug it in, JDM distributor is internal coil too.

Pin designations:
D3 Knock sensor
D6 VTEC pressure switch input
A4 VTEC solenoid valve control
A17 IAB control solenoid valve control

Shopping list:

Here is the shopping list for the swap, its not everything but its most of the weird stuff I could think of. Yup, being thorough isn't cheap. But when you're done you're going to have everything in new or near new shape, like you should want any performance engine!

Accord parts:

-EGR valve- so that the plug on the accord harness fits
-fuel rail, if you haven't done the other options
-you can use the intake if you don't have an aftermarket, or prelude one
-front coolant neck, next to the header (so that the accord harness can plug into it)

Random advice:

Cheap parts. Don't buy them. That means most of the stuff on Ebay. They cost more in the long run because they break, don't fit, or have no support after you put them on, and in some cases all of the above. You WILL actually save money by buying high quality parts in the long run. If you need to save money try to find the good parts at a discount or used. Perfect example: trying to find a gasket for the two piece Tsudo header that I had on the Accord. Answer? You don't because Tsudo blows. The bracket to fit to the block doesn't fit either. Cheap crap...