B18C6 swapped civic won't start HELP!
 

I bought a 99' civic ex coupe with a 01' B18C6 swapped in it. It has a P28 ecu with a Skunk2 re-flash, Apexi v-afc, msd 6al w/ magnacore wires, skunk2 stage 2 cams, aem adjustable cam gears, omni dual valve springs and retainers, CTR pistons and an eagle block guard. I put a mixture of 105 unleaded and 91 unleaded to get a 93 octane ratio.
I've owned this car for a year and a half with no real engine problems until over a month ago. One morning the car wouldn't start, it would crank but not fire. when i got home that evening I put on a new fuel filter cause i had one and it started up. next morning same thing, cranks but no fire up. That evening I put in new spark plugs, cap and rotor. fired right up and started in the morning for a week. Then it started taking longer to start in the morning. cranking for up to a minute to fire. in the evening going home from work it would fire up in less than 5 seconds. One morning it just wouldn't start. I could definately smell fuel and thought it might be flooded. I used my kill switch to disable the fuel pump and cranked the engine. To my surprise the engine started and i quickly flipped the switch back to turn on the fuel pump to keep it running. I was able to use this technique for several weeks to start the car in the morning. In the evenings it would have no starting problems and would restart no problem day or night when the engine was warmed up. A couple of weeks ago i just couldn't get it started, day or night. On a friends suggestion I removed the msd and rewired the TEC dizzy.
Question #1 I couldn't find a good explanation on how those wires go online, lots of harness wiring but not ICM wiring. msd wasn't helpful. When you look at the Hitachi 12-303 ignitor it has three connectors on front and one on the side. I'm calling the connectors from left to right 1-3 and the one on the side is 4. so the connector next to the side one is 3. Connector 1 has a yel/grn wire plugged to it that comes from the harness. Connector 2 has a blk/yel wire that comes from the + connector on the coil. The + coil connector also has a blk/yel wire attached to it from the harness. Connector 3 has a wht/blu wire that come from the - coil, NO OTHER WIRES ARE CONNECTED TO THE - ON THE COIL. Connector 4 has a blue wire on it but it's not connected to anything, I think it's for the RPM gage on the integra but the rpm gage on the civic is connected to the ecu. Is this wired right? if it is I have no spark. When I re-connect the msd, I have spark.
I tested the coil and icm according to Chilton's and the coil failed the secondary coil resistance test. it's supposed to be 12.8-19.2k ohms and was like 550 k ohms. The icm passed all it's tests so Chilton's said to replaced it. I had the guy that built the engine look at them and he said the coil was good(he didn't use a multimeter, he used a test light) and the icm was bad. I dropped 3 bills at acura for a new one(my, my acura aren't we proud of our little part) and it didn't fix it...
Question 2# What the hell is wrong with this thing! The fuel pump primes, the main relay clicks, all the fuses are good. Please help. Any and all ideas are greatly appreciated. Sorry so long winded.