Then, I figured I didn't want weird bacteria or something growing in it, I put it in the freezer over night on as cold as it could get.

Yeah, that's not necessary. Bacteria won't start growing until ~24 hours later, and by then you should have lye in it, whose alkalinity would prevent bacterial growth. This was totally unnecessary. Also, I'm not entirely sure why you moved it to a different jar.

Then left it overnight in the freezer as cold as it could be. There were no crystals in the morning so I figured I had too much naphtha.

Perhaps try evaporating it by letting it sit out.

So I evaporated about half in a wooden drawer with dry paper towels and a desiccant both next to the bowl. The evaporation took a few hours (6hrs?).

Put it in a well-ventilated area. It needs a large surface area making contacting with circulated air.

Then, I put it in the freezer overnight and all day until 4:30p when I got home from work. There looked to be one or two small crystals; so, I left it in longer thinking that keeping it in the freezer would grow more crystals.

Oh lawd.

My first container was left to dry next to dry things because there were visible crystals in it. I removed the lid and placed it in the drawer upside down to left the naphtha dry off. All my crystals melted and evaporated and my glass is left clean.

Did you scrape the bottom of it with a paint scraper or razor?

Did you do more than one pull?