I have mostly bought in person locally, from stock. I bought my all-koa 424 LTD from Martin Music in TN. They seem to be a repository of limited editions, and were fine to work with. They were the only place in the US that still had one a year after they first came out. Taylor sent me their contact info when I was seeking who might still have one in 2007.
FWIW my favorite online shop is Elderly Instruments in Lansing, MI, not far from where I grew up. Three of the four Martin guitars that I have owned came from there, one from the custom shop. Tall Toad in Petaluma, CA is also good, as is Gryphon in Palo Alto, CA. I have bought in person from both of them, years ago. Hopefully these are among the shops you have considered. I only mentioned stores where I have bought from, not many others that I have read about. GLWQ (good luck with your quest).