There isn't a chance you got a rod cap on backwards or two or more rod caps switched between rods, is there??
Also, do you really trust the machine shop??
I had a HD800 bored one time - and it started and ran great - for about 4 minutes - as soon as I got water to the top of the well, it would pull down and stop with a loud squeak!!
Let it cool down - it would start right up - long story short - the machine shop had gotten the cylinders just a touch tight - and as the pistons expanded, they'd lock the motor down...