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I have the notorious 2011 powerstroke, had the valve break and tear stuff up. I bought a new oem shortblock from a dealership last Aug. I stored it in its crate and randomly sprayed fogging oil on it when I could while it took till now to get brand new everything you can think of. It's more than a long block now. I've pulled the engine, cab on and am getting ready to install everything but the short block has super minor rust spots on all the mating surfaces. Cylinder walls and piston tops good to go. I do not want to scotch Brite pad those mating surfaces. Is there a chemical I can use to wipe those spots off that's not strong enough to cause pitting in the surface. Also as far as connecting the short block back to the transmission is there an alignment process such as #1 Cylinder needs to b top dead center and I'm aligning with a mark on the transmission or plug and play.
If it is very superficial rust use a polishing compound, make sure to tape off any opening that are internal.
As far as the transmission the block should have 2x dowels to line up the transmission. All I do is turn the engine until you can see a flywheel hole for torque converter through the starter window then make sure to adjust the torque converter to mate up with it. Lastly use a magnet near your hands when screwing on the torque converter bolts, last thing you want is to drop one of the nuts into the tranny bell housing.
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