After taking the old engine out, take your stock flywheel to the machine shop to have them turn it. You want to have a good surface on the flywheel so your clutch has something to grab on to. If you choose to go all out, I would get a lightended flywheel at this time (or before your swap.)

Now take your old engine mounts off and put them on the new engine, or put your new engine mounts on. It all depends on how much money you have, or what condition your old ones are in. I didnt have enough money for this, so I elected to go with my old mounts. They were in great shape, so I was not worried about them tearing with the new engine.

Next, put your flywheel on, then your clutch. This is where you would use that clutch alignment tool. Next, attach the tranny. Intall the wiring harness on the new engine. Fuel rail; Depending on what kind of engine you received (JDM or USDM) you may need to swap fuel rails too. I got a JDM engine, so the fuel line hook-up was on the opposite side compared to the USDM engine. I called honda and they confirmed that the fuel rails for all model Preludes (92-96) are all the same. So I used the fuel rail and fuel line from my S model engine.

Getting the new VTEC engine in the engine bay is tricky. You need to tilt and angle it to get the damn thing in. Once you are to this point, you will see what I am talking about. Dont give up, just keep at it, but be careful not to mash
anything (ie; shift cables, crank pulleies.) When putting my engine in, I forgot to move the shift cables, and burried them. It took some manuvering to get them back out.