I need help with LC2i install process.

I have it wired in to factory sub wires underneath cup holders DK blue and black. Sub sounds like it's rattling and I've had this issue since I installed the lc2i originally by tapping in to passenger door speaker wires. I just moved it to under console sub wires and now when I turn on rsa the sub is full volume to whichever source the rsa is on. Wtf. And sub still rattles. When I have it with everything set to flat I don't get any sound out of it. Gain is set accordingly with multimeter for my sub 500w rms at 4ohm 44.77V I set it to 44.01..

I'm starting to get very annoyed.

Either I have bass but rattle/clipping or nothing

If the RSA is controlling your sub then you likely have the wrong wires...
If anything pull from your passenger front door. Drivers front door has chimes and rear doors both are controlled by the RSA. 

Beyond that you don't set gains according to a DMM, you set them to sound quality/volume. If your sub is still rattling you may have a bad subwoofer or box that it is in has a loose panel or allowing air to escape from a hole or something.

If you are using a ported box your port could also be doing something wierd. I always use sealed boxes for my subs because they sound smoother and don't have issues due to ports. Sure I could get more volume if I went to a ported setup but just not worth it for me.

Rodney

You certainly can and should set gains with a multimeter, it's the next best thing to an oscilloscope. Gain is not a volume knob. Gain controls how many volts are coming out of the amp and you should set it to your subs rms using ohms law. It rattled on the door speaker too.  Sub is brand new. Box is ported, used.. I may go with the idea that the box is compromised. Which is fine. It's out of an extended cab and is currently behind the drivers side rear seat with the passenger side rear seat lowered down.

My issue however that doesn't make sense to me, is that when the sub is plugged in to a demo unit at visions, it sounds perfect.

I set my gain to sound. My amp is 250w rms and the sub is 300w rms. When I first turned it on it sounded bad, clipping and just generally booming like crazy. The gain was only 2/3 turned up and the radio base was set to half. My gain is now set at a 1/4 and the head unit is set to 2 clicks below max bass and it sounds great.
I tapped into the sub wires under the console as well but I used all 4 wires. both sub channels go into the amp and  I have the amp bridged into 1 channel going into the sub.
Try re wiring your input to your amp and turn your gain down. I think you will be happier.

Might sound silly but make sure your amp is using the high voltage inputs too if you don't have a line out converter from the factory sub wires. That would make a big difference as well.

Here is the wire colors for the 2 channels of the subwoofer for a 2005. Make sure your connected to the right ones. You said your connected to the dk blue and black. Should be dk blue and light green for that side.

First off how do you even go about using a DMM to set gains? If you use white or pink noise they are not the same as real sound waves for one. And you will never match the sound levels of real sound. Normal sound is made of AC waves of varying frequencies.

I attended Metra Installer School in 1993 and received MECP certification of the second of three levels and could have passed the third level but did not have the experience to do so.

At Metra they told us specifically that you could NOT use a DMM to adjust gains because manufacturers don't accurately rate their speakers for marketing purposes. You MUST adjust according to the music. You CAN use an O-scope and watch for the AC waves to become square waves but voltage levels are going to be questionable.

We were trained the following procedure as I remember it...

#1 Start with Gains at minimum
#2 Turn radio to maximum volume
#3 Turn up gains equally until you can hear the radio clearly
#4 Insure that the radio is not clipping, if it is then reduce its volume until it clears up
#5 Increase the gains until you reach maximum gain or the speaker starts clipping then back down  until it clears up.

Biggest thing to remember is to make sure the gains are increased at the same rate if you have separate gains per channel. And due to the fact the speakers will affect the circuit any measurements must be done with the speaker in the circuit.