Head gasket/timing advice

::EDIT::
Engine type is GA16DE JDM swapped 2 years ago


Well, I just finished replacing a faulty head gasket, Im ready to turn the key BUT i need a few advisories.

First, the timing chain, when I initially took the cams out and sprockets and let the chain loose, I marked the bottom sprocket to the crankshaft on the link and tooth which does NOT match the manufactures Shiny link to the manufactures sprocket mark, but is the way it was when I took it apart, it is 2 links off, from my speculations it never matched. but I know it should, i put the head back together anyways keeping my mark in place and aligning the 2 camshaft sprockets to the manufactures link and sprocket mark anyways. my question is BEFORE i crank the engine...am i wrong? should I go back in and adjust that bottom chain/sprocket even though the mark i made is the way it was before i took it apart? I dont wanna bend valves and make what I have finished into something bigger.

Second, on top of the transmission below the air intake there is a hose coming off that I dont remember ever unplugging and I cant find a home for it, I dont want to think that a loose hose is like some sort of air release or something in the tranny. but it literally comes off a nipple on top of the tranny, it is a dry hose, no fluids on it. any ideas? I will take a pic if anyone needs to see it.

Thank you