The threaded rods I received appear to be straight enough, or at least not obviously off. Not like the one you had a photo of.
I don't kinow if the way I used to get the rods parallel may have sounded complicated, but it's actually pretty quick and easy. You can pick up calipers for around ten bucks. They don't work for measuring everything, but the things they do work on, you'll get very accurate measurements down to the thousandths of an inch. If you're already familiar with using calipers, you can skip most of this without missing anything. For those who haven't played around with them, here's a quick YouTube video on how to use calipers:
https://www.youtube.com/watch?v=28qOM0uG7h0
I did about what you mentioned in screwing down the gantry about half way. Then, using the little prongs at the top of the caliper for taking inside measurements, I measured the gap at the top and bottom. When they weren't the same, I loosened the two screws on the motor mounts enough so it was just possible to move the mount, then tweeked it until the measurement at the top and bottom was the same. I don't know how precise their machine work is, but on mine both sides came out to about 1.465" to get the gap perfect from top to bottom. I was actually a little surprised both sides were so close to being the same, which would suggest at least some of their machine work is fairly precise.
Using pretty much the same method, I also used calipers to make sure the height was the same on both sides. Calipers make that asjustment real quick and easy. Just find the short side, lock in the distance on the caliper, then line up the caliper on the other side and turn down the screw until it touches the prong on the caliper -- about 30 seconds work.
It seems to be one of those tools that if you have one, you'll find it comes in hand for measuring a lot more things than you originally bought it for. There are basically three different styles. The cheapest ones don't have a dial, and I wouldn't recommend those as they're hard to read. Dial calipers have a dial to give you the numbers for the second and third decimal places. There are also digital calipers that have a small screen to display the measurement. Give or take a bit, they run around $10, $20 and $30 respectively for entry level models of each sort. I use the dial type like the one shown in the video and have found it works fine for everything I've needed it for.
Anyhow, hopefully the above is useful information and not too far off topic. I gather everyone kind of works out their own methods for doing some of this stuff, so I'll just toss the above in the pot as one of the possible ways to go about it.
PS. Did you ever get the bent rod problem squared away?
As near as I can tell, they use the cheapest threaded mild steel rod they can find to make those. Most hardware stores have a threaded rod bin with assorted sizes, usually 1-3 feet long. If you can't find a replacement in the right length, you could likely find one that could be cut to size. Some stores might even be able to cut it for you. Home Deopt will cut some things, but I don't know if they'll do those. Alternately, lay the bent one on a piece of flat soft wood (pine 2x4, etc.) and swat it with a rubber hammer to see it you can straighten it yourself. Mild steel bends fairly easily, so the main consideration is to not damage the threads if you get to pounding on it. It takes a bit of fooling around to straighten bent metal that way, but you could likely get it straighter than it is if you can't find a replacement.
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