B18B1 into 95 civic dx coupe

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Success on the swap. I have a 94 integra LS motor in my 95 civic dx coupe, running a DC Sports JDM 4-into-1 ceramic header, free-flow catalytic converter, 2¼" exhaust to a tune-able muffler, AEM cold air (fender-type, not the "short ram" wanna-be), NGK platinums, new O2 sensor, new ground wires....

My problem is this: when the clutch is all the way in, and the shifter is in Neutral, i can't get into any gear, and it makes a wierd high-pitched grinding sound when I try to. If you let the clutch out from the floor about 1" (or maybe less), then it's smooth as silk, you can shift into all gears just fine. While in gear, if you push the clutch into the floor, it grinds and doesn't want to ease out of the gear. What's up with this? Shifting is smooth, like it should be, provided that you don't push the clutch in all the way.

See more about my car ... http://mywebpages.comcast.net/95civic/ (no ads! no pop-ups!)
used the shift linkage from the 94 or 95 integra LS. It seems to hit a bracket underneath the shift boot, where we had to put a "shim" to keep it down, away from the body.... it would hit the bracket on the way to 5th, about 1/8" before it was in the gear.

After the shim, the shifter works fine.... i'm wondering why now the clutch doesn't seem to want to dis-engage? every third or fourth time I go to shift, it's like the clutch doesn't fully disengage unless I dance across the pedals and do a little mojo jig. it's annoying when `stangs are trying to race me (due to my exhaust, I would guess), and I come out like a fool because my tranny won't let me shift :-/

frustrated in tennessee

"In this world, there's three kinds of people: Those who can count, and those who can't."
try bleeding the line better ive seen it where u press the clutch in the slave cyl. pushes the fork then u push it in more an it starts to go in sounds like theres air in the line
i figuired out that if you shift below 1800 RPM, then it will shift smoothly. Otherwise, the clutch doesn't seem to disengage properly. If you try to disengage above, say 2500, it will "stick" in gear. i'm wondering if flushing the whole clutch would be neccessary? thanks for advice :-)