Okay, so let's say I am booksmart when it comes to working on cars, and can kinda get by actually fixing them. My girl has a 92 pathfinder and I noticed a water leak. Being the good Fiance I am (and not knowing the mess I was getting into) I offered to fix it for her. Here I am 2 weeks later, Water pump easily enough replaced (after tear down). Since I had to do this major tear down I also decided to replace the timing belt thermostat and the p.s./ alt belts. I did not put the engine at tdc before removing the timing belt, but did put all timing marks in place before installation.

Sorry for the long explanation

Now for the issue I'm having after putting everything back together I did a test start where it ran extremely rough. I assumed I somehow put the timing 180 out somehow (not realizing the timing is controlled by the LH cam), so I took it all back apart and spun the crank 1 revolution. after reinstall of belt and harmonic balancer I did a test start and it didn't help anything.

Did I make things worse by flipping the crank? And if not, where is my issue? Has anyone had this problem before?

Distributor/ rotor/ spark plugs were not fooled around with.

It's hard to say since, obviously, none of us were there when you did the job. If the only thing you did is remove the belt to replace the water pump and now the engine runs rough, one would have to assume the most likely cause is the engine timing is off. You didn't mention if you used a new timing belt or not; you should have! Since the crank turns twice to every single revolution of the cams, you really did nothing by turn the crank one revolution. FYI, this engine is an interferance motor, so you need to be careful when working with the engine timing as you could end up bending valves. On a new timing belt, there are three lines that mate up with the marks on the timing sprockets and an arrow to show direction (should point to the front of the vehicle). One of the lines is "dashed" and is lined up with the timing mark on the right bank, or passenger side, cam sprocket (will be on your left if you are standing in front of the vehicle and looking at the front of the engine). Before disassembling the front covers, turn the crank so that the "0" degree mark is lined up with the pointer on the lower cover. remove the top cover and the cam sprocket marks should "roughly" line up with the marks on the rear timing cover (they never line up exactly on the VG engines). If the marks are on the opposite side of the sprocket, turn the engine one revolution. Now, remove the pulley and lower cover. Install the new belt, loosent the tensioner nut, turn the right bank sprocket counter-clockwise a couple of teeth to let the tensioner take up the slack and torque the tensioner nut to 35 ft/lbs. Turn the right cam sprocket clockwise a couple of teeth and then use your thumb and forefinger to twist the timing belt in the middle of the span between the two cam sprockets. You should be able to turn it 90 degrees. This method lets you know that the timing belt is not too tight. Re-adjust if necessary and re-assemble.

Definitely DID replace timing belt. new belt has instructions saying 40 teeth between cam marks, and 43 between rh and crank, has 3 solid lines (not any dotted ones), also no arrow. but that shouldn't matter as long as i got all the lines matching right? crank DOES match. cam like you said is slightly off on both. put timing marks in line before installation of new belt. also, how likely is it to bend valves rotating crank by hand with no belt?

Days later and still no solution. This is crazy!

First thing is first. Do a compression test on all your cylinders. That will tell you if you bent a valve, which likely happened if the engine cranked and the timing wasn't close to where it should be.

If your compression turns out ok (Mine ranges from 110 psi to 150), then put the timing belt on correctly. That means cylinder 1 at TDC. That means lining up your cams with the marks. The marks on the belt aren't necessary, but are a good guide. Having the camshafts and crankshaft where they should be is what's important.

If your compression is bad, well then it's most likely bent valve and you'll have to take off the heads for that project.

Btw, a quick and easy way to get TDC is putting a screwdriver or such in the sparkplug hole while turning the crankshaft by hand. you have to be careful that the screwdriver doesn't get wedged anwhere or you could mess up the threads or worse. This is not the correct or precise way, but will do the job for a backyard mechanic.