This shit is a lot harder than I thought. I currently just ordered everything for stage 3, (mamba k04s, 1000cc injectors, 525 fuel pump, various other supporting mods) because my ko3s lasted a week on my stage 2 tune. (18psi peak, taper to 12) I still have stock airbox, hitachi sensor, so no scaling for me.

Before I start, yes fueling is overkill but original plan was to go built engine k24s e85.

I am using an M box bin, with map switching (to switch between e85 and 91)

Now the fun part. the wiki is confusing to me. I understand that I need to change KRKTE, which I did for my 1000cc injectors (KRKTE is 34.125/(injector flow in cc/min), leaving mine at 0.03408) and I have set my TVUB as well from what I could find about these injectors online. There's other things I have to change as well right? such as lamfa, kflamkrl, and other things for fueling. I'm really looking for help and advice on doing this for e85, because I don't want to have problems when I decide to use it. If someone could help a major noob out, I would appreciate it.

I understand how and why it works, My mistake for making it seem like I didn't understand that. I'm having trouble understanding what I need to change and what I need to change those values to safely enough to not destroy my engine. Sure I can change LAMFA to .656 for e85 and adjust later but how do I know this is right? I know for gas, 14.7:1 is stoich, and I was using 12.5:1 during WOT in my stage 2 tune, but that was very simple using the stage 1 xdf.

I just want to make sure im doing this the right way

Your questions are still not relevant in any way to what this forum is about.
This forum is about how to adjust values in stock ECU, how the algorithms work and so on.

You are asking basic internal combustion engine questions. Like what AFR should you run. This is the same question whether you have the OEM ECU or not, it has nothing to do with what is discussed here on this forum.
You say you understand how and why something works, yet your next sentence is totally contrary to that.

If you do not understand what fuel enrichment is used for an ICE, then you know nothing about how an ICE works.
Knowing how to bolt an engine together or knowing that the piston is connected to the crankshaft through a connecting rod does not make you a tuner!!! Not even close.

So start with BASICS on how the processes inside the internal combustion engine work. Once you got a grasp of that, THEN you will be able to ask more concrete questions, and most likely you will understand most of the algorithms in the ECU anyway.
I recommend reading some of the books by Greg Banish as a start.