Modify stock ROM

Hey all,

So I've been looking for the answers to this, and the kitchens don't seem to work out for various reasons. What guides I found are incomplete, and rather old. I'm hoping someone can help me with what I need to do to modify my stock rom.

My device: T-mobile LG G3 (D851)

Android 5.0.1 Lollipop

My goals:

Deodex
Debloat (some)
Root (so I don't have to upon reflash)
Zipalign (on boot possibly? not sure how it would impact things)

thinking about init.d support, but I don't know quite what I would do with that.

So I'm basically trying to mess around and learn a little bit, and I'd really appreciate if someone could help me out doing this manually. I have windows installed, and I have debian on my laptop, so either environment is accessible to me.

Thanks,
--Madd

PS - Mods, please move if this is in the wrong area. Sorry if it is. Chef central seemed ideal..