I think you can set every tissue to adamantine by using
[SELECT_TISSUE_LAYER:ALL:BY_CATEGORY:ALL]
[TISSUE_MATERIAL:INORGANIC:ADAMANTINE]
but I'm not certain if you can select all tissues this way, you might need to select them one at a time.
An easier method would be to remove the [USE_BODY_DETAIL_PLAN:STANDARD_TISSUES] and use
[TISSUE:ADAMANTINE]
[TISSUE_NAME:bronze:bronze]
[TISSUE_MATERIAL:INORGANIC:ADAMANTINE]
[MUSCULAR]
[FUNCTIONAL]
[STRUCTURAL]
[RELATIVE_THICKNESS:1]
[CONNECTS]
[TISSUE_SHAPE:LAYER]
[TISSUE_LAYER:BY_CATEGORY:ALL:ADAMANTINE]
But this will remove the other nuances of individual tissues; they will all just be a single adamantine tissue.
FIREIMMUNE and FIREIMMUNE_SUPER tags do not protect materials from temperature effects, they just prevent you from being automatically ignited by fireballs, firejets, magma, and in the latter case, dragonfire. Other temperature effects are caused by HEATDAM_POINT, COLDDAM_POINT, MELTING_POINT, BOILING_POINT, and IGNITE_POINT. You can set these in the creature variation using the same method dragons use (at the end of their raws). Although if you make them out of adamantine it won't matter, as adamantine is already immune to temperature effects.
NOT_LIVING has nothing to do with blood and will not prevent relationships with dwarves, it just makes zombies not hostile to them, and will also prevent them from being zombified if they die. To make a creature not have blood, you just remove the [BLOOD:LOCAL_CREATURE_MAT:BLOOD:LIQUID] token.
Creatures that can fly will always fly, I don't think there is a way to stop this.
I don't know what you mean by "best" HOMEOTHERM, it depends on what temperatures the creature's materials can survive. One notable thing is that if you make it very high or very low, your creature will burn or freeze nearby creatures. Be careful setting it too low, as it may flash-freeze itself if it steps in water.
SWIMS_INNATE has nothing to do with swim speed, it just means they will never flounder due to low swimming skill. Swimming gaits are used to control base swimming speed.
You can make humans spit bullets by replacing [CDI:MATERIAL:LOCAL_CREATURE_MAT:SPIT:LIQUID_GLOB] with [CDI:MATERIAL:INORGANIC:STEEL:SOLID_GLOB]. (Or liquid glob, which will cause them to spit molten steel, or whatever material you prefer.)
Dragonfire is found in dragons, just copy and paste the firebreath interaction.
Jumping cannot be modified, apart from disabling it. Jumping spider men are not actually better at jumping than any other creature.
ATTACK_PREPARE_AND_RECOVER rates are indeed important, they affect the number of ticks it takes to use an attack. You might not notice because the game "skips" any turns that you can't do anything, but you'll get countered a lot less frequently if your attacks are faster.
You can find an example necromancy ability, and other example abilities, on the wiki.
You can make body size however big you want, it depends on how overpowered you want them to be. However, there is an upper limit to size, which is not quite known, but if you make creatures bigger than a giant sperm whale you might see attacks behave weirdly.