What should I get. I have read about the ARMS #40. Does this just mount on the top rail?
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Yes, and it is hands down the most popular back-up sight on AR15.com. Some people don't care for the small aperture with the horizon line though - you can get it with a normal small aperture if that is the case.
You might also look at the Knight's 300 and 600m sights. The 600m is the only elevation adjustable folding sight out there.
What do I need to do when I get the TA-31, is there a mount that will allow me to look under that scope to use the iron sights or must the TA-31 need to be romoved?
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You can mount the TA31 to a detachable carry handle and it will let you use the iron sights through the tunnel underneath the ACOG. Since the TA31 is designed to mount there anyway, you don't have any height over bore issues, although some people don't care for the height of the mount because it affects their chin weld. This would also answer your backup sight question for now.
If you mount directly to the flattop, you'll have to remove the ACOG to use irons and you'll need to buy a mount. The TA51 is the two thumbscrew mount that Trijicon sells for this; but ARMS sells the ARMS #19S mount for the ACOG also.
I've mounted my ACOG to both the carry handle and the flattop. While both had things I liked, I ultimately chose to go with the flattop mount; but it is really a personal preference thing.
Is there a specific mount for the TA-31 that I should get that is optimal for this particular set up? Any recommendations as to who to purchase these from?
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Of all the ACOG mounts, the ARMS #19S is superior in my opinion. It has perfect return to zero capability and can be removed or attached via a single throw lever ($123 shipped from MSTN.biz); plus it has the same small footprint as the TA51.
Sorry to be so full of questions, but I am new at this, and Hawaii (I live on Kauai) is not afloat with shooting ranges or other AR fans.
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I used to stay in a house on Anahola Beach. I didn't realize there was anyplace at all to shoot ARs while I was there. Not the best environment for shooters; but an incredibly beautiful island.