So i'm puttin my bottom end together and i've got the #1 and #4 piston/rods in and it seems like the #4 rod is getting hung up on the intermediate shaft so the motor won't turn. the marks on the rod are on the same side as the shaft as per bentley, anyone know what's goin on? thanks.

Is the IM shaft in all the way?
Seem a few I Shafts that have had the lip broken off letting the shaft float a fair bit.
looks like a pic from the back of the motor with the expansion plug removed(so you can see the gear end of the shaft)
I would guess that it is an issue with not being held laterally by the lip properly.
is it a 1.6 or 1.9 motor?
is the shaft from that motor originally?
-Owen
yea it's the og shaft. i think i got it figured out after a couple hits with a hammer. lol thanks guys.
haha it wasn't in all the way. still turns and came back out. maybe hit was too harsh of a word. how about 2 'gentle love bumps'?? damn machine shop put the bearing with the oil channel facing the wrong way even after i reminded them of it's orientation. might be time for a new machine shop.
they are. thankfully they are honest.
Ok so i'mma take the block back today and i was wondering if anyone knew what a safe clearance would be between the IM shaft bearings and IM shaft? i can't find anything in my bentley about it. I can turn it with a wrench but i can't grab it with my hand and turn it and i would hate for it to get to hot and seize up. thanks.
Be sure to use a quality seal and install it propery in the IM seal carrier, too! I know first hand how fast the oil comes out of there when the seal fails...
I've always installed the pre-sized bearings and have always been able to turn them by hand afterward.
X2.
Should spin by hand. Might be a bit tight, but if you can't spin it with the pulley installed, something bad's gonna happen.
Be sure to use a quality seal and install it propery in the IM seal carrier, too! I know first hand how fast the oil comes out of there when the seal fails... 
Whenever I've installed an IM seal it seems like it wants to pop out until it's all the way seated so you gotta make sure it's completely in.