That is good going greekman
I'm a bit surprised at the RLTC comment as i've read only good things about it and years ago drove an M3(E46) with this and found it to be a revelation.
It is possible that because you have changed so many things at once it is difficult to appreciate what is what and possibly the LSD is interfering with it
The Nismo LSD is a clutch type not TORSEN type FYI.
I'm also a bit surprised about the racket its making and some of the things you are describing are I agree it may be noisy as its mechanical and the right oil may quieten it a bit but you should'nt be experiencing hopping or shuddering etc Atleast the oil change should show a clean oil without schrapnel or excessive bits if not it will suggest something is not fitted right!
Anycase If i were you i will reset the torque at the lowest setting and go from there at the sametime. I will do some research too
You also should bear in mind that you now have stiffer bushings, probably stiffer a suspension setup including the ARB etc so might be worth slacking a notch or so as too stiff is equally bad as i found out.....made the rear jumpy and very skitish even on track
I struggled as I changed ARBs, droplinks, camber and toe arms, 3 way coilies and wider tyres all at the sametime and with despite what i considered a good fast road/track geometry set up It was a big jump from just having only height adjustable coilies with preset rebound and though all the changes i made where sound individually on paper it did not work well.
Ony by restarting afresh with minute changes at a time to each component that i have got the car to where i want it and its now apparrent that i need stiffer bushes and mounts to make the suspension work even better. After this would i consider an LSD though i feel keeping the oem VLSD with RLTC would adequate and advantageous to have, as you get control over the factory TC and can switch the damn thing off if needed. the other thing that i am yet to try is to use R compound tyres like the R888 or advan A048 which allows you to run a more aggressive set up for track but it all becomes to much hassle.
Out of interest did you get the Advance ME RLTC or an standard item from RL?
Do keep the feedback comming
Goodluck
cheers