529T for a 2000 civic sunroof?

I have a "half"answer for you.

You are right in NOT moving the wires themselves to the switch. They need to be attached at the motor, as you have done so already.

I believe you are really only 1 wire connection away (and a relay) from making it work.  On the 529t, there are two activation outputs for each side:

Motor side 1 = Gray

Motor side 2 = Gray/Black

One side does sunroof open, and the other side does sunroof closed.  Which side did you choose for sunroof closed? Side 1 or Side 2? If side one, then you will be dealing with the Gray wire. If you chose side 2 to close the sunroof, then you will be dealing with the Gray/Black wire.

STEP 1:

You have to attach your designated wire (either Side 1 Gray OR Side 2 Gray/Black) to the negative output wire on the car's sunroof switch. You can test for this wire by probing the different wires on the back of the switch while you hold down the close function of the switch. At this point, your car key should be in the proper position so that the sunroof is ACTUALLY closing. You are looking for the one that is outputing a negative signal. (I unfortunately do not know which wire this is). By doing this hookup, you are tricking the 529t into thinking that you are actually there, holding down the close switch (vs the tilt mode), and the entire system should stop at the close position. This wire that you find (at the car's sunroof switch) should NOT output a neg signal while you press the tilt mode. This is how the car knows whether you want close or tilt. Until you join your 529t wire (either Gray OR Gray Black) to the close neg wire on the sunroof switch, the car does NOT see the neg and will always go into tilt mode.  Again, I am sorry that I do not know the color of the wire on the switch itself. My brother has a 99 or 00 Civic, so I could eventually look myself.

STEP 2:

But that is not all. The sunroof switch itself does not operate unless your key is in the ignition position (or is it acc position)? So you ALSO have to wire up a relay from your 529t neg output (Gray OR Gray/Black) so that it can give temporary power to the sunroof switch itself during the close process.  In this step, you are basically giving power to the ENTIRE sunroof switch (since it has no constant power), so that the system can properly recognize what you did in STEP 1. So here, you would have to figure out which wire (on the sunroof switch) needs 12V. Another meter job.

And then there might be the issue of diode isolating if you have a 530t hooked up on the same GWA wire closing your windows. But then I guess that wouldnt be much of an issue if you ALWAYS wanted your windows to close along with your sunroof.

I hope I was somewhat of a help in this long post, and maybe someone who has actually done it can point out the proper color wires on the car for you.