I had the fuel injector pump housing off of my 1990 idi to replace a bad fuel injector line. But somehow I lost my pain mark on my gears and now the truck smokes grey and dies after going to low idle.

So I must have a tooth off.

I'm trying to find out the marks on the plate next to the balancer. I have two holes and a small line underneath the lower one and in-between both holes I have a embossed or stamped circle. Which one do I like the balancer up with?
And how should I go about timing the housing gear up?

 

I'm confused on why you pulled your gear housing off for a bad injector line?

I'm equally confused on why you pulled the IP at all.

This resource has good images of the IP gear information: http://www.blackwire.com/~bjordan/Te....3_IDI_101.pdf

 

Had to pull it all off do to one of the bottom fuel lines leaking at the pump and noticed it leaking oil alittle bit on the bottom of the housing area.

 

Nope, all lines can be replaced without removing the pump gear or housing. I had one of the lower lines crack and leak and replaced no prob without touching the pump or any other lines. I believe I used a crows foot and extension on a 3/8" drive.

That being said, I've heard of people lining up the timing marks without pulling the timing cover but it's not gonna be easy. Personally I'd use it as an opportunity to replace the front main seal and just pull the front cover.

 

I'm having a really hard time grasping this. You had a leaky injector line, so you pulled the IP and the gear housing? Removing an injector line or two is easy as hell in a truck, and I've even done it in my van a dozen times, but can't fathom why anyone would pull the IP. But the gear housing is whole other animal.

As in the link I posted, you can find pictures of how to line it up. It's a PITA though and like the other commenter said, you might as well just redo the whole front of the engine while you are at it.

Next time, don't ever remove your gear housing unless it is ABSOLUTELY necessary. You can pull your IP without messing the gear housing, just undo the 5/16" 12-point bolts out of the gear, and the IP slips right out. But really, you shouldn't ever have to pull an IP to remove any of the lines. I think all I used was 5/8" open ended wrenches to extract my injector lines. If I can do it in a van, you can easily do it in a truck.