Suspicion that I have assembled timing out of time?

Last week - I pulled the timing cover and all - and changed the timing chain, tensioner and guides - no more. Chain had dark colored links for cam gears and crank gear marks. I considered I did a through job - chain stretch was minimal. Did not change cam gears or crank gear. . Renewed ft crank seal. Resealed with the high oil resistance ultra black, Pulled the oil pan, cleaned the rtv out of the bottom, resealed. New valve cover gasket, spark plugs and intake manifold. Replaced the water pump. 2x. 1st the af just poured through as if no gasket - even though that ultra black was used. 2nd sealed up well. I laid the ecu over to one side - and it rained. I falsely believed that the control board would have been a sealed unit with epoxy or rtv between the pins in their receptacles- and came to find out that the ecu became filled with water - where it was laying. Uncrimping and drying out - did not allow this engine to start. I ordered one from a reflasher - and it arrived in today's mail. The engine would not start immediately. Had a horde of stored codes. Cleared them. Engine started. Ran a bit - and things smoothed out. I had complications - 1 was that the brake pedal was and still is hard. I have smoke checked the intake. Put a vacuum pump on the brake booster - and have a normal assisted pedal. I put a vacumn gauge on the hose to the check valve and have 16 0 18 inch vacuum. Pushed a drill bit into the nipple for the hose going to the brake booster - with no obstruction. Drove it down the street a little ways. And back. In the assembly of the chain and gears - I had turned this engine by hand 2 full revolutions clockwise - so that the spring in the tensioner could push out all the slack it could from the chain - and then brought the engine CC back to where I had set it up - reverifying the timing marks on the chain to the cam gears and the dark color link to the crank gear. I felt pretty good with all of that. I did not expect to have any problem. The low vacuum - I can not explain - and I am headed toward pulling the valve cover again and the timing cover again and verifying the crank dot mark and the cams index marks - across from themselves in the slight arch way of the head. I have no belief that I ever would have it so lucky that the dark colored links would ever just line up - and be where I need them to be. So - What I am asking of you - is the at the point of verifying the crankshaft TDC - I know of using a skinny and putting it into #! - And rocking it around - and watching #1 intake valve open and close - but there is just a small bit of motion there at TDC that can be off by a link - I guess. So - As I understand the pointer on the timing cover - there are 3 marks on that boss. Facing it head on - TDC is supposed to be the mark on the bottom right - as per Microsoft CoPilot. - But I don't know this. The crankshaft TDC might be the first mark on the left of the pointer boss. In any event - The engine runs and went up to 4,000 rpm and seemed normal enough. Only one time out of the few minutes of run time did it seem to stumble a little bit - like a plug misfiring and then cleared up. But still low vacuum - no brake assist. The reflashed engine computer seemed to work well. But - I don;t know much of the circuits that are tied into the wiring and - I acknowledge that I had attempted to run this engine with water in the ecu case - where current could go anywhere and did go where it could go - resulting in a no start. The replacement ecu came this morning in the mail 2 days out of Ohio. Now - I had 2 fault codes related to the electric throttle body - P2122 D circuit and P3237 E circuit that never would clear by scanner delete. Removing the negative battery cable cleared those out. But there was yet another fault code that has appeared - that has not been there before doing the all of this - and that is a low voltage fault in the brake light switch. I've tried removing this fault several times - and it will not go away. I have replaced the switch with a new one - and - I did not expect it to go away - and it did not. . As I read - one of the suggestions is that the body control module has a fault. And before I do any more changing of parts - I am just chewing on what I can do - short of taking a razor blade and opening up the wiring harness wrap from the BCM to the brake light switch to look for a melted wire that may have happened when the water logged ECU was attached. Yes, I saw when I attached the last battery terminal - back when I wanted it to first run - a current path draw. I knew I was in for a ride of trouble. I just did not know how far it was going to go. In the mean time - Saturday last - I received Camber adj bolts, o/s tie rod ends and the lower left control arm - and worked to replace these items - in preparation for a FEA - to stop the inside tire wear that is happening. I am pausing to take a breath. Getting a bit tired of all that I have worked to do - but know I need to go further on down the track - to the next train station - before I can get off and be happy. I do not know if any of this you may have heard of or experienced or wish to even address. And if you don't - I can understand why. So - first I need to verify the actual position of TDC for the crankshaft - and verify the camshaft gear oblong marks facing themselves - under the valve cover. If they are off - I will need to pull the cover and set it up again - which is the only reason that I can begin to understand - the why of having low vacuum volume. The PO572 Brake Switch Code - If we lean toward a BCM - then shouldn't a similar model with the same heated seat option being coded even to a different VIN - do you have any experience that the BCM may function as needed - or - from the front side of asking this question - would need to be programmed to my wife's VIN on this Jeep. All of this - that comes from my wanting to know that I know that the whirling whine that comes out of our power train was not timing chain, tensioner or serpentine belt, tensioner bears or idler bearings. I changed all of it - at the 140,000 miles point. 5,000 miles ago - I changed the transmission pan, the filter in the sump and the thermostat filter on the outside face of the transmission for the cooler lines - hoping to put an end to this particular set of high-pitched whine kind of sounds. Truly - Truly - I did not wish to pull this CVT transmission out of it - as we bought it - with a factory reman installed some 40,000 miles ago. Listening to the whine through the front timing cover - made me think - it was timing chain related. The alternator clutch seemed tight and had to red rust death on the front face - that would have justified replacing it while it was all in the open. The output I witnessed was a 14.2 V - just before I quit checking fuses as the thermostat opened to bleed the air back through. So,
Timing mark verification for the crankshaft. BCM - because of current path of electric running anywhere due to water in the ECU - and the PO572 fault code that is not the fault of the brake switch. What do you think? Something you might have support that could go somewhere? Or spinning my wheels - already worked it to death kind of job? I may have to cut off the sheath of wire wrap and go searching to find if there is evidence of any wires that may have gotten hot enough to melt the insulation off the conductors - But - knowing what to expect on which pins of the present BCM might prove or disprove the need for deep surgery like I may be facing. Yes - a DVOM and doing pin checks has been my efforts since I first learned about the Datsun 280Z fuel systems.