Fuel filter shutoff not working 2k 6x4 diesel

Hey everyone, happy new year. I am having the craziest thing happening to my 2000 6x4 diesel, first it kept stalling and I removed the fuel lines, fuel transfer pump(lift pump), fuel filter and housing and all the lines going into the tank. I also drained the tank but used a siphon to do this as I did not want to remove all the necessary items between the seats. Anyway, I found some "Gelantinous" substance on the pickup screen in the tank. After cleaning all the lines, filters etc.. It runs again HOWEVER, now I can't get the fuel filter "shutoff" to stop the flow of fuel to the filter. Crazy stuff eh, I was hoping (because my JD service manual) does not seem to show the fuel lines clear enough for me to follow if anyone has a diagram or info on how the fuel lines are routed. I have figured out that the pickup line goes to the fuel transfer(lift) pump and then back to the "inlet" on the filter housing. The filter housing fuel outlet is supposed to go to the injector pump but my injector pump has 2 connections (one of which seems to be on the end of the banjo bolt with the injector return lines(over flow -return). I just can't figure out which one of these is the TRUE inlet to the pump. Also, WHAT WOULD CAUSE the engine to continue to run? one more thing, when I PINCH the fuel return going to the tank the engine will spit and sputter and finally die... is my fuel filter house jacked? Another thing I noticed when I cleaned the fuel pump is that is has a "feed back" valve and it is working... so is the gator drawing fuel from the "return" line? I replaced the O-rings on the fuel bowl and shutoff handle, I am seeing a very light seepage around the bowl nut but not very much. It seems to be getting fuel from somewhere to keep running... (crazy thing, like I said it left me stranded on the road and now the damn thing won't stop - I think it is possessed, LOL). I did search this forum like I always do but found nothing relating to this issue.

Thanks for any comments!

Thank you,
Gatorboy65
2000 JD 6x4 Diesel (560hrs)