Jeep Strokers

Ok ive been reading a lot here over a few days then i joined up a couple hours ago cause i cant find what im looking for.
Sorry this is going to be a bit long winded.
I bought this 91 yj with a 4.6 from a guy that had it sitting for years in his driveway. I just got it drivable. Lots of bad. Fuel system was a mess from rubber bits in the fuel tank a rusty pump, bad injectors etc. It had Ford injectors so i replaced with same. Its got an msd6a box on it with a stock distributor. Its also got all the smog on it so it passed California emissions. Intake looks like a its off a 98. Got a nice stainless Thorley header.
It sounds bad like a diesel, it has horrible spark knock at higher rpm with my foot in it, 3500 rpm or so. From what ive read it looks like regular fuel is a no no. And thats what ive got in it right now. I will be putting premium in it from now on. put a dial back to zero timing light on it...had to take the fan off to get it close enough to see...(old age is a bitch), anyway im seeing 15 btdc at 1000 and it tops out at 40 btdc...which from what i see here is too much. So im not quite sure the best plan of attack. Would a new stock ecm fix my timing issues, im concerned its been tuned and has a different fuel map and if i change that it might not pass emissions, or maybe im barking up the wrong tree. Im not one to just throw parts at a problem, hoping for a fix. I know ive got an engine teardown in the immediate future but no point unless i fix what caused the problem to start with.

You might want to check if the bolt holes of the crank position sensor have been slotted to allow the ignition timing to be advanced. It's possible the previous owner lived at a higher elevation, used 87 or even 85 octane fuel (thinner air = less risk of detonation), and advanced the timing to regain some performance.
You'll need to reset the timing back to 10* BTDC at idle with maximum advance at ~34* BTDC by adjusting the CPS clockwise when viewed from the front.

thanks for the info btw. finally got some time to fool with it again. I did a deep dive on the manuals and everything else i could find. Low and behold the IAT sensor is reading megaohms....so it thinks its freezing outside...according to what the service manual says it will advance the spark if its cold, I was unable to find out how much it advances it but im hoping its why my timing is off. So im going to replace it and see if it fixes the issue. The CTS was in spec. so not sure what the pcm thought about the divergent readings. Ive got my fingers crossed. I went from carburetors straight to obd2, only vehicle i worked on that had this flash code system was a Citation...back in 1980. so figured the sensors were all good since i wasnt getting a check engine light. its the old Assume again...