If the crankshaft binding is truly caused by a head-heads being mounted then there most likely is a problem with a piston. 
The information starting with the subject title is confusing. Why would one be working on a "new engine"? 
I guess this "new" refers to different one. 

Does the engine not turn at all or is it limited to less than one full turn or two full turns?
Moves but less than one turn, something with crank, rods, pistons. 
More than one but less than two turns something with cam gear, cam shaft, or valve train. 
On water boxers common valve train issues are the push rods not being seated in the lifters and my favorite the clip communing out of the lifter and plunger falling out and getting jammed in the slot in the lifter bore. 

If the crank does not turn at all I would start at the flywheel end checking the end play shims and that thrust plate. A little grease will help hold it all together while torqueing the flywheel-drive plate down. Always check and turn the crank while torqueing the flywheel-drive plate and stop at the slightest sign of binding. Crushing that tang on the thrust plate can damage the engine case.  

Another fun item that can cause grief is the distributor drive gear. With the distributor out turning the crank forward can push the gear up. Turning the engine over can also let it fall out. The gear then can get wedged on the crank gear. There are also shim(s) on the bottom of the gear. These can even fall out and get jammed. If they fall and can’t be fished out the engine will have to be disassembled. 

I have even seen things get dropped into an engine. Last year I, yes me dropped an oil breather nut into an engine. I thought it made it to the floor. It got whipped up onto the cam gear and wedged between the crank and cam gear. Busted the cam shaft instantly. Embarrassing indeed. 

Hope this helps,
Happy New Year,

Dennis

-----Original Message-----
From: Vanagon Mailing List [mailto:vanagon@gerry.vanagon.com] On Behalf Of Ken
Sent: Thursday, December 31, 2015 1:05 PM
To: vanagon@GERRY.VANAGON.COM
Subject: Re: New engine won't turn - 2.1 WBX

Don:
What if the camshaft timing was incorrect causing valve to piston interference?
Ken 

-----Original Message-----
From: Vanagon Mailing List [mailto:vanagon@gerry.vanagon.com] On Behalf Of John Rodgers
Sent: Thursday, December 31, 2015 5:30 AM
To: vanagon@GERRY.VANAGON.COM
Subject: [VANAGON] New engine won't turn - 2.1 WBX

Engine turns beautifully by hand on the bench. Put the new AMC hesds on with all parts assembled, torque them down,  and the beenengine won't turn.

Removed the heads twice, still no joy. Sounds like a valve stuck in a guide to me.

Any body else ever had this problem or got an educated opinion?

Thanks.

John