Ok the problem is i don't know if my msd box is working properly or its just my distributer. Sometimes she'll crank sometimes she wont and not get any spark. Once i apply spark to it it starts right up. The MSD coil is working properly i believe. My question is wiring just the coil and overriding the MSD Box. I just use the red and white wires from the distributer directly to the coil right??? Red + White - ????

 

First you need to state what MSD box you are talking about. Second, I'm confused when you say you "don't have spark, then you apply spark and it starts right up"
Also, this sentenceis a little confusing; My question is wiring just the coil and overriding the MSD Box.

Finally what engine do you have. I have wired up three friends Hondasand none of them had red and white wires coming from the distributor. Unless you are talking about the wires you added in. Inside the distributor the two wires you are using are the white/blue trace and the black/ yellow trace. Also the black wire is actually the + and the white is the negative -. If these are hooked up backwards the car wouldn't start.

 

The MSD Box is the 6a i also have the MSD Coil Blaster i'm not using the distributers stock coil. The wires that are on the MSD Box is Red and Black that go to the battery and ground, there is red orange that is positive and negitive for the coil blaster, and there is red and white (added) which goes inisde the distributer connected to the wires you stated, that old coil used to be connected to but is now connected to the external coil blaster. About the spark thing i made it to a garage to get my welds on my exhaust fixed and it cut off on the rack and wouldn't start, so the guy had me try to start it and he did something and it started right up, he said he just gave it a little more spark i believe literally from the batter to a ground or something. I have the b16a2. He (the mechanic) thinks that the box isn't firing correctly so i'm trying to bypass it, i know it can be done because i had to do it before, although it was awhile back and i'm confused as how to do it again. Then again it could be that the box is fine and the coil blaster is messed up, anyways either way if i just bypass that box and use the external coil that would tell me if it is the box by running or the coil by not running.

 

That is a good first step. Just bypass the box and hook the wires coming from your distributor to the coil. If it still doesn't fire up then your next step might be to check the coil or the igniter module inside the distributor.

I just had this problem and I went through the same steps you did. My car would crank, but it wouldn't start up. I had spark, but it was a dull orange color instead of bright blue. These are the steps I went through;
1) I disconnected the SCI and ran the wires straight to the coil. Still got nothing and now I have no spark at all.
2) I bought a cheap coil from Pep Boys and hooked it up. Still nothing and returned the coil.
3)Bought a new igniter module installed it and the car fired right up.
4)Hooked everything back up including the SCI and the car has been running great since.

This happened the day after New Years so it has been functioning fine for the last month and a half. I own a '99 Si so I also have the B16A2. Good luck and hope this helps.