6 bolt swap starting issue

[1G9S9T7]

I just did a 6 bolt swap and I am having trouble getting it to start. I have a 97 GST. Here are the engine details. I got it out of an already swapped 2g. The engine was pulled from a 95 GSX and it was started up and running before it was pulled. I used the instructions found on this website to do the swap. I changed all the sensors like the instructions stated from the 7 bolt originally in the car so I knew for sure each one was switched. My CAS harness is the one for sale on Magnus's website for the 97-99 eclipses. When we got the engine in the car, it would only turn over but not start and I was missing a ton of different lights on the car. The battery was near dead during the attempts when it would only turn over (the under dash lights and rearview mirror lights were getting dim). I had the battery charged and it was brand new, only been put in this car when we tried rebuilding the 7 bolt before swapping to the 6 bolt. After the battery was charged, we put it back in and tried turning it over, all I got was a clicking noise and eventually nothing. During the time the battery was being charged, we investigated the wiring and I found a plug with the wires loose in it. It was located under the thermostat housing (right below the upper radiator hose under the cap). There are two plugs I think right next to each other in that location. I followed the wire color code and got another plug off a harness to wire it in. I remember a post somewhere under a search I did for a "no start 6 bolt" talking about a wire in that location but I really couldn't understand it. I also investigated all my fuses and found a blown one, I changed it out and I got power to almost all my lights I was missing except for reverse lights, tag lights, and turn signals (I do have hazard lights). I checked all my fuses and everyone of them showed up good. I also checked every ground I could find. Does anyone know what's going on here or what I have done wrong?? I have tried to be as detailed as I could with my problem and I have searched for hours over the past week for answers but can't really seem to find any other than my turn signals may have a broken switch. I wanna check every easy thing I can before I start trying to replace that switch. I don't know if the missing lights are related to the engine not starting or if there is a bad ground I overlooked... and that plug under the thermostat housing. When the car was turning over, it was getting fuel but I didn't get to check for spark because I figured the low battery would be the first thing to fix. Any help would be much appreciated and I have the gsx still if there is anything I can use off of it wiring-wise. (It was badly wrecked btw as I will probably get ppl saying "why didn't you just leave it in the gsx".. that's why).

 

[1G9S9T7]

UPDATE
I checked all the things in the forum I found about not turning over and discovered a starter wire loose (always something simple). I got the car back to turning over. My friend checked for spark and confirmed that all four cylinders had spark. I had taken off the AFPR and put the stock one back on (fuel poured out of the rail) and I took the plugs out, they were wet and smelled of gas so it seems to be getting fuel (My dad said it wasn't but I question his judgement). As I read through a lot of other posts similar to mine, they all talked about the cas and 180* off. I figured since mine had came out of another 2g running that it would be fine. I decided to check it. I found several images showing the 180* off and lined up for TDC and when I pulled the cas out, it was 180* off. Something posessed me to take the valve cover off and when I did, I found a rocker fell off and was laying in the head. Upon trying to recover it, several more fell off. These were on the intake cam. I researched about it and it seems everyone has been saying if that happens, I pretty much bent a valve. I tried to turn the crank by hand and it goes so far and stops like it's hitting something. Any input?