3406e miss, fresh out of frame overhaul, break-in?

Hello! First of all, thanks to anyone who takes time out of their day to read my issue! Just completed my first overhaul, a 5EK 3406e in my 1997 Freightliner. With 2.2 million on the clock and 1.2 since last overhaul, it was time, power was low, a partial miss in one cylinder... Engine came out of truck and while at the machine shop getting block decked, gears re-bushed, crank checked etc etc etc, the head was found to have a crack in the exhaust valve seat, so new head went on the engine, along with new spacer plate, injectors (cat reman), turbo, fuel lines, pretty much anything that I could replace, I did. New Cat fuel pump, new oil pump. IPD steel overhaul kit. Spent a lot of time getting the cam gear lash just right, bolted down new spacer plate with spacer gasket underneath, liner protrusion was 3.75-4.25 all across the deck with freshly milled block. Only one liner flange seat was found to ever have been cut on this engine, minimal milling was required. Engine went back in truck, started fine, had a miss at idle, and whenever you goose it off idle, it would miss and puff grey smoke on one cylinder. Since it smoothed out when it was warm, Cat ET wouldn't let me do a cutout test until 149 coolant temp, I manually cut out cylinders and poked the throttle until I came to #6. No smoke with 6 cut out, so I replaced that injector. Super annoying to get a bad injector from the factory! No sign of pinched o-ring on injector. Engine now idles smoothly, runs smooth when warm, but still has a stumble when you poke the throttle, until it warms up for 10-15 minutes or so. It's winter time, super cold here in Colorado. Was kept in a heated shop that won't dip below 30 degrees at night though. Am I missing something here? Do I just need to break this engine in and quit sweating it? Maybe the rings just need to seat? Any advice appreciated!

 

Also, prior to overhaul, I rebuilt the front end. New springs, king pins with bronze bushings (no-ream, just had to be honed a little so pins would fit in after bushings were pressed in), tie rod ends, wheel bearings, brakes. After getting the engine put in, the power steering acts like it is getting no fluid even though it is full. Steering wheel barely moves, seizes up when I turn it, almost like it has no pressure. The king pins were not tight, and I could turn the spindles left and right easily by hand before putting everything back together.... is there a special bleed procedure that needs to happen when the pump has been out like during my engine overhaul?

 

That's good to know, I've overhauled John Deeres on the farm and they always took a little while pulling their weight to get up to snuff power-wise, anticipating the same here with the big Cat!

 

Thank you all for all the help! I will check for air bubbles and it dawned on me I have a rig for bubbles in the fuel I'll try out tomorrow as well. Yep the drive sleeve for the power steering/fuel pump is there, with fresh o-rings to boot. Is it odd that you can throttle up normally and it doesn't miss when it's warm? Only that it does it when it's cold? It would always miss slightly when it was bone cold in the mornings if you poked the throttle but would smooth out, I don't recall it ever missing with a puff of smoke when it misses though. The cam was polished and checked at the machine shop, and they say it didn't show virtually any signs of wear, and the machine shop said the rockers were all good to go too. No scuffs or marks, and still tight to the rocker shafts. The injector height was set with my height tool as well, book says 3.07 inches? It is my first overhead though, so I'm definitely not ruling out my skills here. I set the intakes at 15 and exhausts and jakes at 30?

 

I'm missing the part of my binder full of 5EK manuals where it goes over the cam timing sensor, does that need to be recalibrated after overhaul?

 

Both new harnesses too, injector harness and engine wiring harness, ET says no diagnostic codes