I'll do my best to answer these questions but im just figuring out ships my self and only just got past the stage a head of where you are now.

Hardpoints: These are little triangles placed just inside the ship. You have to name them right to get them to be used in the game. Something like hp/something/HpTurret01, the paths in the cmp file of other models. just type hp instead of hardpoint and it will add them correctly. By default the game adds the object to the closest surface to the hardpoint so even though the hardpoint is inside the model, the turret is not so to speak.

Also HpMount should be placed at the bottom of your ship, this is used as way to tell the game where the ship will touch the ground so it doesnt sink into the deck.

Only Hardpoints showing.
Now this is a problem that I still have and it meant my ship didnt take damage from lasers too. Lizard came to my aid and told me to copy one of the other models sur files and rename it to match my models name. I still have the problem of only the hardpoints showing but the model now works correctly and takes damage correctly.

You will probably hit that problem next, so remember the solution.

Theres a few posts kicking about explaining more about this, my advice is, if this info has not helped, do a search.

Giskard

My model takes damage correctly, so I haven't hit that yet, It's mainly just selective hardpoints, specifically, CM01, HpEngine01, and (I don't really care) the ConTrail ones.

I'll try that sur file thing and see what happens, Thanks

Forget it, I figged it, I didn't put Hp in front of Engine or CM01, Kicking self now...

Lol, happens to the best of us

Giskard

the disapering ship issue is fixed by changing the lod ranges in shiparch.ini
from
LODranges = 0, 40, 60, 140, 300, 1000
to
LODranges = 0, 999999
only do it for your ship though.
custem ships dont have Level Of Detail models funtion yet.