I just installed a new front wheel (Araya aero 1) and also took off and reinstalled my front brake at the time (Shimano BR-1050 105 side pull single pivot). I set up and centered the front brake like I usually do and everything looked good. Now when I brake I get a bad "jerk" feeling once every revolution. Holding the front brake while stationary and trying to move the wheel forward I can see the brake arms move forward a bit, there is some play. The wheel is fairly true, there is a little wobble to it but not even close to the old wheel which was seriously bent and out of true yet the same front brake worked perfectly on it.

What should I be looking for here? I tightened the recessed mounting nut and it didn't help also checked the rim surface which seems just fine.

"NEW" front wheel probably has an obvious rim seam or dent.
Flip the wheel and see if the problem changes.

shipping greases/etc on the rim surface. Clean the rims with rubbing alcohol and you should be set.

I was going to say rim seam issue too and flip it around. If the problem goes away, then issue is pretty much resolved.

You can sometimes gently sand the seams smoother.

I had a front wheel that did that. It was perfectly true and no seam on the rim. However, there was one part of the rim which flanged out a bit on both sides which caused the awful brake shudder. The rim was unfixable.

You noted this was an Araya rim. Is the joint pinned or welded or both? Sometimes it's hard to tell. I know the biggest problem I've had with new Arayas that were welded is the case where the joint is narrower than the average with. So the rim brake sinks into the rim, grabs and increases friction on the expansion in width and this happens every revolution. I've never fully gotten rid of this effect but was able to minimize it by doing as others have suggested: a) flip the wheel around, b) change brake shoe material, and c) sand and groove the rim (or ride off road in gritty conditions and use the brake a lot). I still have those Arayas (RM20's) but a few years ago, during a ride off road, I was coming down a steep single track and ran over barbed wire that punctured the rear, and braking hard on the front to slow down while riding on a flat was a tricky maneuver made harder by the rims going "thud" "thud" "thud" and grabbing at the weld. I went and bought some Sun Rhyno Lites in 1.75inch and built another set just out of being pissed off with the emergency braking performance. Problem solved.

There's two causes for this in my experience:

A: Rim seem defect or other defect.
B: The brake isn't tightened down enough--this could either be on the recessed/hex nut or on the middle axle nut.

Both will cause jerking or clicking.