Looking at the magma spear stats now in the skill editor, and it's got some very confusing values. For some reason it has "requires dual wielding" set to true and is listed as a non looping skill, both of which are obviously not true ingame...these are vanilla values by the way. What is going on? These values are in the main skill section, the level 1-15 entries have different values.

Hey, Question! 
You have too many questions. 

-How do you edit globals.dat using GUTS?

You can do this using any text editor, Notepad++  for example.

-Make summon skills de-summon existing monsters

This is possible.
I'm not sure whether you can do it, but you should have 2 different effect.

[EFFECTS]
[EFFECT]
<STRING>ACTIVATION:DYNAMIC
<STRING>DURATION:INSTANT
<STRING>TYPE:DESUMMON MONSTER
<STRING>NAME:MONSTER1
<BOOL>SAVE:true
<FLOAT>MIN:100
<FLOAT>MAX:100
<FLOAT>NO_LOOT:1
<FLOAT>NO_DIE_ANIM:1
<FLOAT>DESTROY_BODY:1
[/EFFECT]
[EFFECT]
<STRING>NAME:SUM_MONSTER2
<STRING>ACTIVATION:DYNAMIC
<STRING>DURATION:INSTANT
<STRING>TYPE:CAST SKILL
<INTEGER>LEVEL:1
<BOOL>SAVE:true
<FLOAT>MIN:100
<FLOAT>MAX:100
[/EFFECT]
[/EFFECTS]

-Edit a current mod (which is in .mod format), assuming this is not a mod you created yourself

Yes, you need to unpack the appropriate mod. If a mod has some "non standard" things, errors may occur.

-Double the amount of armor on all equip, without editing each piece of armor individually

Just change the graph ARMOR_PLAYER_BYLEVEL_FORSET.DAT

-Does anyone have any clue what some of the graphs do in the stat line editor? Stuff like "armor player by level for set" are very ambigiously named.

See above.

-I tried to make coup de grace ...

I'm not so good with skills.

Also does anyone know how item requirements are determined?

Well, the requirements depend on the graphs ITEM_*STAT*_REQUIREMENTS.DAT
Lines
<INTEGER>STRENGTH_REQUIRED:50
<INTEGER>DEXTERITY_REQUIRED:100
mean % for the relevant Item level

   <INTEGER>MIN_RANDOM_ENCHANT_SLOTS:2
   <INTEGER>MAX_RANDOM_ENCHANT_SLOTS:2

<INTEGER>MIN_UNIQUE_ITEM_SLOTS:10

Uniques obviously don't have a minimum of 10 slots either...

Well, I suppose it's other slots.  Not "socketable"-slot, here means "affixe"-slot. UNIQUE_ITEM can have 10 affixes.

I tried putting hp regen 1 in globals.dat and it shows up as 1 hp/s ingame, but it obviously regenerates WAY faster than 1 hp/s...what gives? Is there another way to do this? I tried giving the player units a passive effect with 1 hp/s regen, but it does nothing...

See how it works for the dummy. You need to make a correct effect. Our wiki

TARGET_DUMMY.DAT
[EFFECT]
<STRING>ACTIVATION:DYNAMIC
<STRING>DURATION:ALWAYS
<STRING>TYPE:HP MOD OVER TIME
<BOOL>SAVE:true
<FLOAT>PERCENT_TO_HEAL:1
<FLOAT>TIME_TO_HEAL:0.1
<FLOAT>TIME_TO_HEAL_MAX:0.1
<FLOAT>MIN_STOP_AT:0
<FLOAT>MAX_STOP_AT:1
[/EFFECT]

For example, canons are always generated with at least a certain amount of knockback, but what decides that? I don't see anything in either the item editor or the spawn class that says "hey, generate with this affix all the time".

BASE_CANNON.DAT
[EFFECT]
<STRING>ACTIVATION:DYNAMIC
<STRING>TYPE:KNOCK BACK
<BOOL>SAVE:true
<FLOAT>VALUE:50
<BOOL>NONMAGICAL:true
[/EFFECT]
[EFFECT]
<STRING>ACTIVATION:TRANSFER
<STRING>TYPE:STUN
<STRING>DURATION:2
<BOOL>SAVE:true
<FLOAT>MIN:35
<FLOAT>MAX:35
<BOOL>NONMAGICAL:true
[/EFFECT]
This is a parent for all cannons.

Speaking of affixes, is there a way to find one by the effect? I want to edit ALL the mana regen affixes, but the vauge names in the affix editor are causing me to miss a lot. I can see ingame that there is an affix called "Focusing" that is mana regen, but i can't find it in the affix editor because most of them have very unhelpful names like add_any_200 whatever that means.
I've already done all the ones that say "mana" but i must have missed some...

Well, yes it is a complicated and time-consuming work. No one promised it would be easy. 

Spells : Is there a way to get them to scale by player level? Use owner level/mastery graph doesn't work for some reason. Really struggling to make the damage spells worthwhile because they are weaker than your own skills and stacking passive spells like adventuring is a much better option.

I think you need to rework spells and add this feature.

Weapons : I want to give crossbows a piercing missile, it doesn't look like i can do that via affixes, so i want to edit the missile itself, but i can't find out what missile they use or how to restrict it to crossbows only because the item editor just doesn't have that information. Any ideas?

GUTS\MEDIA\MISSILES\
Real Arrows
Study the forum, study other mods, study the wiki.
http://torchmodders.com/wiki/doku.php?id=missiles

You try to understand everything in a short time, it's impossible. Do all step by step. 

Thanks for the replies guys. I've been looking at the wiki but there's just way too much info missing...and the official documentation doesn't even include a full list of tags and what they do. It doesn't help that both GUTS and the game code appears to have been cobbled together with no standardization involved...the skills editor has a very handy search feature, but NOT the affix editor for some reason...

I managed to figure out how the heal spell worked. For some reason it scales using a graph even if there is NO graph defined under "graph override". Most affixes do this as well and there doesn't appear to be a way to see what graph they use by default?

Using an effect to give players HP regen : The problem with adding an affix to players seem to be that they don't affect existing saves, only characters created after the mod is activated. Is there a way around this?

Is there a way to open the base weapon files in GUTS? I don't see that option anywhere...i can see what base weapon file a weapon type uses, but there is no option to open it in the item editor...

Missiles : I know how to make a missile piercing, but the problem is i can't tell what missile the crossbow uses. That's not included anywhere in the crossbow files that i can see...i'm looking at the real arrows thread but i don't understand what it does, is it implying that the bows/crossbows ingame do NOT use "missiles"?

Spells : Does anyone know how to make them scale by player level then? As both mastery graph and use owner level do not work, neither does setting the stat to experience level.

I've opened up a couple of mods to take a look and managed to get some ideas...for example i opened up "deeper pockets" to try and add a sort button to the shared stash. I did it exactly the way the other sort buttons were done elsewhere except that they are set to shared stash, and i can see and click the sort button ingame, but it does nothing whatsoever...anyone happen to know why? They have the same scripting logic and inventory controller setup.

I'm currently trying to figure out why i cannot remove sounds from pets...i have made a mod that removes it for the pets using the monster editor, and i can see that they do not have idle sounds, but ingame they STILL have idle sounds...do i need to do something else? It is driving me crazy. The crab and jackal pets spam their idle sounds every couple of seconds which is really annoying.

I also tinkered with editing transmuting recipes a bit...does anyone know if there is a way to make the socket recipe work for socketed items, but only if it has 2 or less sockets?

Also i was trying to figure out how the fire rate of looping skills work. Looking at magma spear, it has two entries set to "minimum cooldown 500" and "duration 180". How does that work out? The actual cooldown per shot is obviously not 0.5 seconds, since i can fire at least 3 shots per seconds.

I also just found that pet/minion boost effects do NOT affect minions summoned by your pet...they only affect your pet or minions summoned by you. I can make an affix like "share the wealth" that targets unittype "pet" i guess, but that would ALSO affect other player pets which i want to avoid. Does anyone know a way to make the skill work for only your pet + minions summoned by both you AND your pet, regardless of whether the spell is equipped by you or your pet?

Some other stuff i've been thinking of trying if its possible :

-Make pets auto loot everything just like how gold is automatically picked up by your character

-Make pets auto attack smashables

-Anything that can be done to improve AI as monsters seem to ignore your pets in most situations, making it unnecessary to buff their armor/hp to keep them alive since you are going to draw all the aggro anyway.

Thanks, that seems simple enough.

Okay can someone explain this to me...i set the haste spells as "dont create" and set their rarity to 0. Yet i can still get the spell from transmuting. Why? I can't get the old TL1 spells via transmuting this way, and they simply have "dont create" checked.

I feel like i'm being trolled...

Thanks, i will try doing it with a blank unit type just in case. Its really weird how it keeps spawning even if its set to dontcreate though...just in case, mods at the top of the load order are loaded last and will overwrite everything before it right?