!! Work In Progress !!
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NEW!
I made a single bottle rack.
I also made a new bottle model. It should be printable, but you will need a tall print volume.
Used the Brewstir to propagate your yeast? Well now you have to wash and drain your beer bottles. Luckily, I have just the thing.
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I may cut holes the solid parts to save material. The bottom should remain solid, of course. It's canted to drain water towards the opening.
Wait, try the 2nd version, it's in 2 parts.

!! Work in Progress!!
Version 3, a single bottle rack. You should print up two and glue them side-by-side, but oriented in opposite directions, so the bottles lean in the opposite direction from each other. This will help balance the rack.
Use the version 2 if you are going to print it; glue the second piece in with super glue, hot glue, or PLA. It won't fit every beer bottle; I have been told that Grolsch (I think?) bottles are an odd dimension. I may remodel the bottle for general accuracy (and to make it more realistic).