I recently took off the Castle nut that holds the tie rod to the knuckle and the threads got messed up. I bought a replacement M12x1.25 castle nut but it is too tall for the cotter pin to be used. Does anyone know where I can buy one of the shorter style castle nuts? Or should I just buy a M12x1.25 tap?

Here is the new vs. old, as you can see the new is about twice as tall. 

 I think I'd try shortening the nut (temporary fix until the proper one can be sourced)) or drilling a new hole in the new location if there's enough space to do so.

A nylok style nut could also work just fine. As long as the taper of the joint is properly seated, the chances of it coming apart is pretty much 0. Remember how much work it was to get that joint apart. 

I have about 20 of those stock castle nuts I've saved for some darn reason, but hardly practical to mail you one... 

I think I might have the answer for you...

https://www.belmetric.com/stainless-castle-nuts-c-3_558_1376/cn8ss-castle-nut-stainless-steel-p-8342.html?zenid=3j9n5fjlbd4p3hntj7jub44nl5 

Looks to be a lot shallower than what you bought, although maybe not quite as shallow as the Nissan OE item.

I've bought from Bel-Metric before.  Good vendor, good products, great catalogue.

BTW, if all else fails you should maybe pay your local Nissan dealer a visit.  This might be a PN that's still available.

I found one on Amazon that was M12x1.25 and it fit, so all good now.