The number one rule of buying a guitar is always, always, always play the thing first.
That's fine if the shop in town can order in any guitar you like but if you're buying a handmade boutique instrument that isn't always possible. Now there's this thing called the internet and we can buy stuff from all over the world but until we can play a guitar on another continent we struggle to obey that number one rule, but we can get close. Here's the rub.
Know what you want.
Do your research, learn the jargon, be able to communicate with people that talk the language. What's a pup? What does action mean? 3 string or 4 string? Tuning?
A trusted endorsement
If you can't get to play the thing, can someone you trust do that for you? Can you communicate with them what you want so that they can check those things out for you.
A video
Can you access a video, with quality sound, of someone playing the instrument. Are they playing it fluently? Even if you're a beginner you'll want a quality instrument that can be played well by someone who knows what they're doing. Be wary of too much distortion or other effect, you'll want to hear the guitar, not the amp.
Components
Get on to ebay and search for pickups, machine heads etc. Learn to distinguish the good ones from the cheap, nasty ones.
Reputation
Does the builder have a good reputation? This shouldn't be a clincher because it's easy to manufacture a reputation online and there'll be plenty of more modest folk who will make quality instruments, but if your builder is well known and has a lot of endorsements then they must be doing something right.
Is the builder a player?
Again there'll be plenty of exceptions here and you can build a great guitar without knowing how to play it. An experienced player however will know exactly what goes into making a guitar sound and feel good and will translate all of that knowledge into their instruments. Plenty of experienced non-players are aware of this and have taken the advice of players and refined their techniques over many years.
Remember that the bottom line is how the thing plays. You want a neck that feels smooth under your hands, you want it to play in tune, you want a smooth action on a fretted instrument, you want your right hand to sit comfortably on the box, a player will be able to tell you all of these things. It's not just going to hang on the wall.