Well, after spending the entire weekend doing this timing belt and abusing my hands - it seems you just follow the Ford TSB and if the tensioner alignment moves after/while you fully tighten the camshafts, just let it go.
I re-did the camshaft/tensioner alignment until literally everything stayed in alignment after 2 full engine rotations, and the car ran, but idle was horrendous and timing was obviously off (makes no sense to me still)
Re-did it again letting things lie where they seemed to want to go - and so far the car has been running great with no noticeable issues.
So for future reference to anyone who may end up confused like myself over the mis-information etc via videos and tutorials online the way to set the timing belt (at least in my 1999 Ford Contour 2.0 VCT) is as follows :
-Remove all necessary parts to get to timing belt
-Loosen tensioner, remove/replace all parts you are (i'd highly suggest replacing the tensioner and all of the pulleys, not just doing the belt)
-Put engine to TDC with either the screwdriver in cylinder 1 trick, or do as I did and use the "special tool" Ford calls for to keep the crankshaft from moving (screws in right behind the Catalytic Converter and offset down to the left of the crankshaft (could be cam) sensor that is right behind the Cat as well)
-Loosen the camshafts (intake camshaft is 50 ft lbs and is the cam towards the windshield, exhaust camshaft is towards radiator with the VCT hub inside the gear and this has a cap on it at 20-30 ft lbs, and then has a inverse torx inside that holds the camshaft - I did as others suggested and used a 12 point 16mm socket to loosen and tighten this)
-With camshafts loose, use the second "special tool" and rotate camshafts towards radiator until you can fit the tool in the end of the camshafts to hold them in place, and in correct alignment
-With the tool holding camshafts, put on the belt and set tensioner to the proper tension by aligning the mark on the tab that goes into the engine to keep the tensioner in place
-Now you can tighten the camshafts (I chose to leave the tool holding the camshafts in place - you may want to remove it so you have less chance of ruining the camshafts) but hold the camshafts on the hexagon that is at the front of the intake cam and towards the center of the exhaust cam with a 1" wrench (size of the hexagon, not size of the entire wrench) torque the exhaust e-torx bolt to 30-40 ft lbs, then tighten the intake cam fully to 50 ft lbs, and then finish tightening the exhaust cam to 80-88 ft lbs
-The tensioner alignment mark may have moved, but from my weekend of hell this seems to be the case, so just go with it and remove the special tools
-Rotate the engine 2 full rotations (720 degrees) and reinsert the TDC pin that holds the crankshaft in place, rotate until it stops against the pin
-Check the alignment of the camshafts again, the tool should atleast slide into the intake exhaust camshaft with no problems, the exhaust cam might be "slightly" off but that I think is to be expected since the VCT gear controls the movement of the exhaust camshaft. Again the exhaust camshaft should only be SLIGHTLY off, as in, it's nearly straight on for the tool to go in, but just will not due to maybe a fraction of an inch of being offset.
-If you got this far, and things seem smooth belt wise (no kinking, no jumping in the belt) you should be fine to put everything together and start the engine. Or you can do as I did, and half re-assemble everything just enough so you can run the engine for a minute and see if the belt walks off or if there is any issues.
I'd say you absolutely cannot install the timing belt and tension it with the cam gears tightened already, as this was my experience (I tried re-aligning the tensioner and doing it with the cam gears already tightened but the car just ran like ••••). Others may have had better luck, but my experience was simply that the gears must be loose when tensioning the belt, and the alignment mark must be set properly with the gears loose otherwise you will have trouble with timing. Again i'll stress that the alignment mark on the tensioner will most likely move once you tighten the cam gears. At no point was I able to tighten the cam gears without the tensioner mark moving.
