murray195

I've run into some issues with my engine swap and would really appreciate some direction and troubleshooting from you experts out there (this is my first honda build). The car is a 1997 Honda Civic CX hatch with a 5-speed. It had a D15Y7, but the transmission went on it (lost every gear but fifth!).
Now for the good: I had a D16Z6 sitting in the shop with a transmission mounted to it and pretty much ready for a swap. Its a VTEC out of a 1995 civic si. The whole setup has just over 80 000Kms.
So, thinking this would be relatively straight forward, I went out to a wrecker and pulled a computer and engine harness out of a 1998 civic si because I was told that the engine didn't really change from 1994 to 2000.
I had some issues with the driver's side engine mount because of the mount on the engine (which is pretty well incorporated throughout the whole driver's side of the engine) was different from the D15Y7 (the holes in the mount have to be closer together on the original for the D16 to sit apparently!) So, after a little fabricating, I got that mount made and holding very strong.
I am running this car pretty much bare-bones and have left out having power steering and A/C (thats what highspeed and windows are for!). Anyways, this harness seems to have a number of extras which is one of my issues with this swap. In theory, this swap was supposed to be straight forward, but I'm thinking that these extra plugs on the harness (that are partner-less on the engine side of the swap) may pose a problem. I don't know if they're for the 'luxuries" of the car or if they are a necessity for it to work.
So I guess what I'm saying is an engine wiring schematic would be a lifesaver for me at this point!
Now onto the most terrifying part of this whole swap...
I heard the fuel pump pressure up ...interior and exterior accessories work flawlessly ... the engine turns over just fine ... but there is a knock ! This is obviously bad, but I just don't know how bad it really is. I didn't attempt to actually start it, I was just cranking it over, and like clockwork, there's an intermittent thumping coming from the engine area and the whole setup is shaking a little with that thump.
The fluid levels are all good, the pressure plate isn't binding on anything, there's plenty of power to the starter, and there's theres fuel pressure. However, the engine doesn't seem to be drawing fuel and i'm thinking that it's vacuum lines. But I need to know what that thump could be! It's not valve noise or anything like that... this is solid-intermittent-thumping.