Since my tube mount is completely custom, I have to manually align the tube with the first mirror. The C02 laser is invisible (and dangerous) so aligning it correctly can be a trick. I saw a solution on buildlog that I thought was a very clever hack. The guy used a reprap to print out two disks the same diameter as the tube. One disk has a very small center hole, the other has a hole that exactly fits a laser pointer. He mounts them in the brackets and adjusts the laser to shoot through the small hole, into the first mirror. Once the alignment is correct, he loosens just one screw to remove the disks and insert the tube. At that point, the alignment should be very close.
I have a reprap but I had some time to kill before Christmas while I was waiting for my power supply to arrive and needed some lathe practice. I turned these two 'cookies' and bored one to fit a cheap laser pointer I have.
When I started trying to align the tube, I found I couldn't get even close. Eventually I realized that in the original configuration, this plate screwed directly to the end of the RF tube. That would ensure that the first mirror was perpendicular to the axis of the laser. Without those screws, this whole periscope, bends out of alignment. You can actually see it tweaked back a bit in the picture below when I was test fitting the tube.
I'm sure this is a completely ugly hack, but I added a piece of aluminum angle with holes drilled and tapped to match two of the holes on the periscope bracket. I attached it to my mounting rails. By turning the screws, I can pull the periscope back toward square and by turning one or the other, I can slightly twist it.
After playing around, I eventually got the cookie, laser pointer, bracket arrangement to fire the laser all the way through the beam path.
Next I carefully mounted the tube and connected everything up. With safety glasses on, I carefully hit the test button while holding a piece of paper over the mirror path. Once it was hitting the center of the first mirror, I adjusted the mirror angle until it went all the way down the beam path. After aligning with the cookies, it only took about 45 minutes to have it hitting very accurately all the way.