"Are there any basic graphical (mostly to ship) tutorials so i can move around some guns and such?"
If you have 3Ds max, there is a conversion utility floating about on this forum that lets you change .mesh files to a viewable, edit-able file-type. I know very little about modeling though, someone else will have to carry that torch and show you the ropes.
"How would i go about adding new abilities to ships that have none or creating new abilities/buffs?"
Ok, this is a lengthy one. There is a section at the end of every frigate/cap ship .entity file that lists their abilities. You can add in new abilities here with impunity, and then create the abilities in notepad. In order to do that, you will have to understand how the ability/buff system works. Basically, abilities are anything a ship can do that isn't move or fire a weapon. The ability are a vehicle for the delivery of 'buffs,' which determine what actually happens.
Ability files determine who is a valid target for buff effects, what range the ability will have, when the AI will use it, how much antimatter it costs, and the cool-down, among some other more minor things that will become aparent when you view the files.
Buff files are the verbs in your whole operation, they determine what actually happens when a unit uses an ability. They involve doing damage, adding status effects, the duration of said effects, the conditions by which said effects terminate, all that stuff. They can also be used to generate other buff effects, so you can have buff-chain reactions.
Basically, copy/paste is your friend. Once you look at a few files in notepad, and try editing some stuff, you'll learn abit about the language, and you'll figure out how to make new abilities/buffs simply by p[atching tags from other abilities/buffs together.
"Or if its possible to make it so that each ship can learn a single (or more) ability once their made to add a level of customization to each ship you create?"
Basically, it can only get abilities three ways. It is made with the ability available, you research it in an upgrade, or the unit is a capital ship and it learns the ability by spending a "level-up" point on it. Also, point of interest, to my knowledge nobody has figured out a way to get mutually exclusive abilities. Like, if he's using ability a, he can't use ability c. There may be some clever work-arounds, but there doesn't seem to be anything in the engine itself.
"Is there any way to make it so that when a ship gets reduced by x% then it has 100-x% chance of being destroyed? "
Sort of. There is no way to make global rules like this. But you could tweak with the ability/buff system to make it increasingly likely that any ship with that ability would die as his health got lower... It would be a furious pain in the ass, and require one of the valuable 'ability slots,' but it would be possible. PM me if you're interested, it would be really F-ing complicated.
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A few notes on the weapons damage system:
All weapons (and damaging effects) have a DamageAffectType tag. This can be three values: Affect shields and hull, affect hull, and affect shields. You could make your plasma weapon idea work by making a second 'ghost' weapon that dealt %20 of the damage of the orignal weapon, but had a DamageAffectType tag that limited it's damage to shields. Set SynchronizedTargeting to TRUE, and it will fire alongside the main weapon, and just give it blank effect values, so nobody will ever know it was there.
You can see how to accomplish the rest of these things fairly easily by just tweaking this around. Watch out for the shield mitigation, since anything that directly affects hull will bypass the shield mitigation as well, so you'll want to nerf the damage appropriately.
To add status effects, like DoT's and stuff, use the TEC Marza dreadnought's incendiary shells ability as a model. Also, try checking out the LRM frigate's AoE damage abilities, they work more or less the same way and might provide some insight.
Anyway, I hope all that was helpful to you... PM me if you have any questions. Just try to be specific as possible, and I'll do my best to help.