2000 EX wiring harness issue!!! HELP!!!

[johsymar]

I had a d16y8 with 160000 miles in my 2000 civic EX and i blew it up, so I bought a new d16y8 with 50000 miles in it like 2 weeks ago and swapped it. When I had both engines out I noticed dat some plugs in da harness of da new engine were kinda bad, so i decided to cut da gud ones from the old engine and replace them. I put the new one in and fit perfectly, so I bolted everything, but then I noticed that I have 2 extra plugs in the wiring harness of da new engine and couldnt find anywhere to plug them in, one is located underneath the distribuitor, and the other one is located on the far upper right of the engine bay. Anyway so I tried to crank it up and I couldnt, the starter was good but I noticed there wasnt any fire goin to the spark plugs, so I messed around with the distribuitor and cables but nothing, so I decided to try the old distribuitor and see if it worked and I noticed that the plug of the old distribuitor is different from the one in the new engine! Also I noticed that the intake and exhaust manifolds are slightly different from the one I had... Can anybody tell me what can I do to get that car running????.... I will take pictures tomorrow and put them up so anybody can have a better idea of what I'm saying...PLEASE HELP!!!