Putting a copper bottom (made of individual plates) on a model like this is a big, time-consuming job. I'm not at all sure I'd recommend it for a first sailing ship project - and one that, by definition, is only going to produce an extremely approximate model of a ship (which, after all, didn't really exist).
If you want to try it, though, it can be done with thin sheets of copper, cemented into place with contact cement. (I've got a model of H.M.S. Bounty, based on the hull of the ancient Revell kit, that I "coppered" this way about 35 years ago. The cement seems as strong as ever. ) Sand off all the detail on the underwater hull, leaving a slightly rough surface. Do some research on the proper pattern for the sheets. (It isn't as simple as it looks.) Cut the copper (I used .001" sheet, which was available in those days from Model Shipways; a modern source is any company that sells supplies for making stained glass windows) into appropriately-sized pieces, and go from there.
Model Expo sells thin copper in rolls, with a pressure-sensitive adhesive on the back. I used it once on a model with a cast resin hull, and was pleased with the results. (It's lasted about ten years now, with no ill effects.) The strips are far too wide, though, for the scale you're talking about. If you want to do the job to scale, the plates will need to be about 1/16" wide and 1/8" long. It takes a whole lot of plates like that to cover the hull of a ship like that.
An alternative that actually would look pretty good on a small-scale model like this, if done carefully, would be to sand the hull smooth and paint it to look like weathered copper. Back in the days before plastic kits, modelers used to do that routinely on solid-hull models.
Unsolicited suggestion: Before you commit yourself to anything like this, think carefully about the nature of the project. You're building a very approximate model of a ship that never existed. (There's nothing wrong with that - but it surely doesn't call for the same approach that a superbly-detailed, hyper-accurate scratchbuilt model of a real ship would.) If you try to fix every feature of that old kit that doesn't match reality, you'll end up almost building from scratch. (I spent almost 1,000 hours on that Bounty model; in retrospect I might as well have built it from scratch.)
The subject of rigging thread is complicated. One suggestion that, I think, almost every serious scale ship modeler would agree with: junk the thread that came with the kit. Then you get into the problem of what you should use to replace it - a subject that's complicated and loaded with personal opinions.
In fifty-plus years of ship modeling it's never occurred to me to melt the beeswax (or parafin) on a rigging line. Go to a sewing supply store and buy a little cake of beeswax inside a little clear plastic case, with slots in its sides. Pull the thread through one of the slots and leave it at that. (Or use a type of thread that doesn't need to be waxed. That's another subject.)
In a recent thread another Forum member offered a newcomer to ship modeling a fine piece of advice that I rarely have the nerve to offer - but it's excellent advice for anybody branching out into a new form of modeling. KISS - "Keep it simple, stupid." I didn't say that, but it's a phrase worth contemplating.