wouldnt the half axel just get in the way...wouldnt it just push out my left axel out farther than it needs to go?

one more thing....are both of my axels suppose to be the same size?

"does that piece connect to the tranny and then i connect the axel i have to that half axel on one side..then the other side to the left wheel?"
exactly. The two axles should be close to the same length. The half-shaft usually comes connected to the engine when they give it to you. People at PepBoys are idiots, make absolutely SURE they give you both axles for the 1.6L DOHC VTEC '99 Civic Si. If they gave you the right axles, the driver side one should be ALOT shorter than the old driver side D-series axle, bigger too.

"Why not just swap the engines instead of swapping the transmissions too?"

Lots of reasons:
1.) It's a different series engine, it has a different bolt pattern for the transmission.
2.) The tranny is geared better for performance; shorter gears.

i think they did give me wrong axels then...cause the driver side one is so long that if part of the motor werent in the way then it would be able to connect directly into the tranny...with out half axel.

yeah....i got the right axels this time...those guys did give me the wrong ones. all i need now is just a new shit linkage...the half shaft thing... distributor...starter. all of which im getting tomorrow. i just bought a 99 civic si ecu off ebay for 66 bucks..thats with shipping!talk about lucky! also i need a wiring harness. other than that..ill be done with this swap shortly.....yeah it took time but the reason being is because i could hardly ever work on it cause i didnt have the parts i needed. but now im finally getting them. YEAH!!!!!!

Damn, sounds like you'll be rolling in no time. The only obsticle in your way after you have everything bolted up MIGHT be wiring, like if you forget to plug something up, but it sounds like it should start up first try! Props on taking your time again, sounds like it's really paying off. Keep us posted.

Thanks D15,
Shorter gears are good, I get tired of hearing quarter mile passes in two gears.

hey..if i remove the catylic converter of my car will it pass emissions?

Not by a longshot. (In other words, no)

depends what smog tech you have that smogs your car

I know a middleman who has a connection in the DMV who can pass your smog, and give proof of insurance and stuff so you can register ur car. If your interested ill give you his #.

it has already legaly been smoged with the origional engine

I'm dealing with smog bullshit right now, best bet in my opinion is to just find somebody who will illegally do it. Slip the dude a $50 to look the other way and write you a certificate saying it passed. I'm trying to register an out-of-state car in cali, and with my swap and mods...it's not passing. I even bought a cat and it still didn't pass and all the parts they can see are CARB exempt. You have to pass a visual inspection, so all your shit has to have CARB EO numbers on it to be legal and you must retain all original emissions equipment (cat, etc). And then your lucky if you even pass. Smog is so homo, i dont see why they wont pass my econobox civic but will pass a gas guzzling suv, makes no sense...

Yeah smog is a bitch, when i had my legend, it wouldnt pass smog cuz of the EGR Actuator, so my dad tok it to a garage eh knew and the guy just passed it for the hell of it, of course, i crashed it a week later =\