Turns out it was the wrong freaking part. The amazon seller I got it from sent me a part for a non EX 2000 Civic. There was no way in hell it was going to fit.

I had to find a ride to an autozone and got the right kit, in duralast. The sucker popped right in. An entire day and a heck of a lot of tranny wrestling wasted.

LESSON LEARNED: Triple check compatibility, no matter who says what, and always test fit.

We thought we were going crazy there for a bit! Thanks for the support, it really, actually helped.