I'm at a very similar stage. I make a similar amount at my day job and I've sold probably just over a dozen pieces, only for people I know, at an average of $400 each or so. I rent at a community woodshop which has its pluses and minuses.
I'm probably not better suited to answer your questions than you are, but here's my take:
1) I don't worry about anything like that, I've never asked for money up front since they're friends/family. I track the expenses like all my expenses so I know how much the wood costed me if I want to factor that into the price I charge. And I sincerely doubt the IRS gives a crap about the nickels and dimes we'd pay in taxes after you factor in all the expenses we could deduct, so I don't bother with that either.
2 & 3) I think you have the right idea. It's not your customer's fault if you take extra long to build something. If I know something is gonna be a pain or take a while to build, I give them a pretty high price. Shoot, if I don't like the design they want, I give them a prohibitive price and offer a design I like better at a price they like better. I also consider how it would look in their space. That's the beauty of doing something you love on the SIDE (or being FI), you can actually do something you believe in without worrying about having enough.
Also, I don't plan on using eBay or etsy because of shipping eating away at profits - not to mention they're a bit of an amateur trap. Hairpin legs and "shabby chic" everywhere. There are exceptions though; JeremiahCollection, hedgehouse.
And I'd wager a guess that very few go to CL looking to spend a decent amount on custom furniture. They might scour CL for something like an Eames or Risom, but I know guys that have built tables and dressers that have been on CL forever.
When I don't have a waiting list of friends/fam to build for, I might look into an option like that... but I'd rather not. Honestly I'd rather give something away and feel like a million bucks than spend half the cost to ship it or wait for a call on CL.
My plan is to grow my business slowly and surely, eventually working my original designs into some of my projects. Whenever I have a full line of original photo worthy designs built, then I'll consider myself open for business to the public.
Rather than trying to hawk my furniture via eBay/etsy/CL, I'd rather rent it out to home stagers, event planners etc if it doesn't sell right away.
Well, however far you want to take it, all the best. Keep us updated with your milestones.
Edited to list exceptionally good etsy furniture builders.