[RMMZ] Are there any templates for 16x16 Tilesets?

The layout of each tile sheet is the same, just each tile is smaller.
You could shrink the rtp tiles to 1/3 size and draw over them if that's what you usually do.

Notably the auto tiles use the VXA - MZ format not 2k3 so you wouldn't be able to use those tiles directly from 2k3.

Font Texture

You should be able to use one of the other plugins out there to change the font in a message (e.g. Yanfly's message core in MV) and this one to override how the font is drawn.

Code-wise, the first thing that happens in Window_Message when a new page is started is resetFontSettings (which switches font name and size back to default). After that, you could call
this.contents.fontFace = "name of font";
either through a message escape code, or by hooking something like loadMessageFace() to set the font automatically by some logic.
(e.g. change to harold' font when harold's faceset is used)

[RMMV] Parameters + and - HP (flashing red when you walk)

In Game_Screen there is this function:
class Game_Screen
  # * Start Flash (for Poison/Damage Floor)
  def start_flash_for_damage
    start_flash(,0,0,128), 8)

So you could probably override that to do nothing to prevent those flashes

Is it possible to make a skill like "Blade Beam" in VX ACE?

What I've done in the past is to have one skill trigger another. So the initial skill is a single target attack, and it triggers another skill which is the multi target attack.
Not quite what you want here, unless you want the initial target to be hit twice.
Common event in a skill runs last btw, after all other effects of the skill.

[RMMZ] The Stupidest Thing I've Ever Seen

Check if you've used 300 instead of 3.0 when you meant 300% somewhere in a plugin setting.
The editor uses percentages, but in engine normalized numbers are used (so 1.0 is 100%). This makes the math easier, but if you use a large 100x scaled number by mistake it multiplies up to give silly huge numbers like you're seeing.

[RMMV] Need help with making the Level 5 Death Skill from FF5

set the damage to a flat 1, it'll do 1hp damage and/or kill

[RMMV] Need help with making the Level 5 Death Skill from FF5

That probably means your actor's hp has been set to a strange value (like infinity or Not A Number), which could be a problem with a damage formula.

Item Crafting

1) Is there an easy way to disable item categories in the script?

There isn't.
The script re-uses Window_ItemCategory, in create_category_window.
You could replace the Window_ItemCategory with your own window that has fewer options; or change the scene to not have a category window at all and jump directly in to the specific category.
But there's no built-in option for it.

2) How can I change the sound effect that plays when you make an item?
By default it seems to be "Decision3".
I tried to comment out the 2 uses of "Sound.play_ok" and add a ""Bell2", 50, 100).play" right after, but that didn't seem to work.

This seems like the right track, you could also try Audio.se_play.

[RMMV] Need help with making the Level 5 Death Skill from FF5

Right, so change addstate to addState and it should work.

The red text is called a stack trace.
The first line is the actual error "TypeError: b.addstate is not a function".
The rest of it is showing all the function calls that led to that error happening. When debugging more complex problems than this, it would help understand what happened.
The underlined text shows the file and line number (they are also clickable links)

The second error about isDevToolsOpen is an incompatibility of Yanfly's plugin with MV 1.6.1 and can be solved by updating those plugins. It's mostly harmless though, it just means the wrong error is displayed on the screen when the game crashed, but you can find the right error using the dev tools as you just did.

[RMMV] Need help with making the Level 5 Death Skill from FF5

Press F12 to open the dev tools window in test play to see the error properly in the console tab.

I think I typoed addState as addstate.

The console window should show you that with something like "addstate is not a function"