I was trying to keep it broad because the main question was:
KeyStore - Signing - ZipAligning
This was a painful experience for a noob to be undertaking... -_-
I hate this part so much. Download an old version of java (which u need an oracle business account to get!) because the new ones don't work. I can't remeber what else I had to download at this point, think I ended up with 3 versions of Java XDK, Android XDK, Intel XDK and something else... ALL JUST TO SIGN THE BLOODY THING!
When doing it manually, save a notepad doc of EVERYTHING you do.
I used notepad ++, (shift, ctrl,right click to get cmd in the location required)
There's a tiny program floating around somewhere that can do all this rubbish for you. It's less then a few MB!
Advanced+ApkTool+v4.1.0+By+BDFreak
First dozen times I tried to do this I went through the entire process (with a miserably slow net speed) just to keep getting told by google that my apk wasn't zip aligned correctly or something. Days... not just hours..
So yeh I'm not having fun
Hahaha LOL. Had the same experience with Advanced + ApkTool and I also have slow internet download especially upload speed. It was a pain testing those all out because I don't want IntelXDK to make me a Keystore automatically but in the end I just went back to IntelXDK to auto-sign my apk for googleplay didn't accept my apk for it isn't signed correctly.