Am I able to modify weapons to only damage shields for example? Create flak/Missile barrages on command (via ship abilities) Can I make weapons that punch right through shields? Can I create weapons that disable ships or functions (engines or a special ability)?
Yes to all. In the last case, a basic weapon can only do damage, so any disabling effect will have to be an ability. Though really, you can assign weapon effects to abilities (just look at Kol's gauss blast for example), so you can make an ability function as close to an actual weapon as you'd like.
How can I length the time it takes to 'jump' from planet to the next and add a cool down for jumping.
Each playerrace.entity file (playertech.entity, playerphase/psi) has a hyperspaceData section where you can modify phase space speeds, antimatter costs, charge-up time. You can't create a cooldown such that they won't be able to jump at all for that duration, but you can increase the charge-up time so you have longer to kill them.
Finally how can I modify the way the graviety well
I can't give you a good answer on this because I haven't messed with it, so I honestly don't know how far it can be taken.
As per maneuvering, currently what you're asking is not possible. Most unit behaviors we don't have access to right now. They're tied (as best as I can tell) to the entityType definition. So anything defined as a Squad gets to do strafing flybuys, roll around, etc. Anything defined as a ship is pretty static-y. For now, there's nothing we can do about it.