I was installing the bearings on the rods and i noticed a bearing sticking above the mating surface of the cap I checked to make sure the bearing was seated and aligned properly and it was. Should I or could I file the end without the key flush with the mating surface.

 

Don't do that... the act of torquing them down will crush them into the proper location.

 

The rest looked fine I thought maybe I had an odd bearing the rest seam to fit flush on both sides of the bearing.

 

you don't have it in backwards do you? the little tab on the bearing shell engages a slot on the block. all of them i ever put in pretty much fit flush with the block or cap

 

The bearing half is not quite seated in the bearing tang
on the bearing bore. Be sure it is square to the bore and lined up with the groove or tang in the bore and push it into place.
Bearings are a few thou of an inch bigger than a half a circle.
When you bolt the cap on the two bigger than half bearings "crush". This bearing crush is what keeps the bearings from spinning.

Check your bearing clearances before buttoning up the pan.
If anything doesn't seem right, fix it.

rods should have .002 mains .002/.0025 +/-.0005

 

DON'T file the end. You need all of that material to maintain oil pressure at that journal and prevent spinning the shell in the rod.

Make a note of the problem. Torque the cap, then disassemble it and inspect the position of the shells again. If there is still a fitment problem, clean the cap and rod. A little laquer thinner in the end of the rod before assembly will clean off a lot of that varnish that may prevent proper bearing seating. Reassemble the rod, then break it down again for inspection. Rod bolt torque is not so excessive that you will damage the fasteners by retorquing them. Besides, they haven't even been hot yet.

If there is still a fitment problem after a thorough cleaning, it IS possible that you have a defective bearing shell. Given your experience with the APR bolts, it wouldn't be a total surprise. You seem to have the "luck" for that kind of thing. I wouldn't hesitate to ask for a new set if you find a problem there.

Just a reminder to the rest of you reading this, wear latex gloves when you handle the bearing shells so your skin oil/acid doesn't contaminate the soft metal cladding on the bearings. Early bearing failure can result from etched bearings.

BTW - that whole bearing fit issue gets really tough to call with the factory cracked-cap PM rods. You just can't tell where they're sitting. Boy, was I confused... (doesn't take much)