Did the lift screen cleaning and mmo get rid of the code? Did you get to hit lift?
Try and locate the noise (pinpoint) by ear or use a stethescope. I use a real long screw driver held up to (handle pushed against) my ear and keep touching the other end in different places around the engine while it is running. Just don't stick it in the accessory drive belt, lol. This will transfer sound quite well to help pinpoint location. I have a wild hunch it is timing chain noise. The chain tensioner is on the firewall side just below the head on the passenger side. It goes thru the block there and they are known to wear. I'll bet you have some oil in the area as well as the o-ring on it tends to leak over time as well. Easy job to swap it out with two 10mm nuts. Search on here, I'm sure the job has been explained by someone.
I think these 6 speeds are notchy at best. They are not slick and smooth like other Asian manual transmissions. I currently have two GT's and they both feel like the same crappy shifting you mentioned. I did however, on both, drain the gearcase and fill with Amsoil 75-90 synthetic gear lube and this does make them behave a little better. The drain and fill can be done faster than you can locate an Amsoil supplier in the area.
I spent most of my life hunting and fishing, the rest I just wasted.