Well hi Iron Giant
I have some answers for yah I think
To answer your first quesiton no you can't alter your fighters to attack multiple ships because it is assumed they are acting in squadron level (makes no sense for 1 fighter to be able to hurt a capship)
1. Don't stack 1,000 fighters I stack at most 20 heavy fighters and find that MUCh more versatile especially with rocket packs.
Why on EARTH you would stack 1,000 fighters is beyond me and I didn't even know THAT was possible
2. Wrong again here, think about the size involved and in late game the weapons a beam slashing across a fighter group should be able to kill an entire fighter swarm if you have good sensors. It's a good balance and ensures if you use fighters you need to think before you swarm.
As far as fighters against a small fleet of battleships having no chance again wrong "depending on what you arm your fighters with."
You simply need to go for smaller squadrons instead of one UBERSTACK.
In my current game (the one my story is about) I repeatedly sliced through entire Phong Capital ship squadrons with small fast fighter squadrons of my own until shield tech came about and my PDF fighters became obsolete.
So many years later (game wise and about a year later RL wise) I designed a heavy gunship capable of hurting a capital ship, in fact 5 of my new gunships can destroy an SD. However they are only capship killers and would get eaten alive by fighters.
My advice to you is arm your fighters with rocket packs to act more like "bombers" then fighters.
If you want FIGHTERS go for guns and use these only to cover your bombers else wise you might as well not build sub-capital ships at all.
Also don't rely on fighters on a planet to save your butt unless that planet has weapon platforms, fighters are NOT meant to act on their own.
This isn't star wars or WWII where fighters have an uber advantage over cap ships SEIV is much more "realistic" in the sense that fighters and cap ships would in RL both move in 3 dimensions and have roughly equal maneuverability (given the proper engine/mass ratios). So a fighter cant just "dive bomb" a ship and get away with it.
A fighter in SEIV requires heavy guns or at least a mothership to back them up and get them close to the enemy before launch elsewise it's like sending an army of ants against a beatle with a flame thrower.