CEL, Code 52, no other symptoms ???

[BigBoox]

Ok, here's the short hx, bought a 90 4runner in 9/13 with 173k. It's a 3L AT, very clean, had CARFAX, truck spent most of it's life in Va Beach.
Less that 1000 miles in, blown head gasket. I live in remote NNY, no real Toyota service close by. Nearest Toyota garage wasn't too interested in replacing engine. No machine shops within 120 miles willing to look at it, w/o a ton of $$.
Bit the bullet, shopped and bought a rebuilt 3VZE from Phoenix engine rebuilders. Found a good Mechanic(used to work for my regular garage guy,I knew him from years ago). He is ASA certified, works primarily on Commercial Vehicles for a large local agency. Also has a garage and small business on the side. He takes on the job, fitting in as he has time, and I'm not in any real hurry as I was recovering form a bad fall. Calls me 2 weeks ago, got it running, has a code 52, he is going back in to replace the harness. Replaced harness, replaced Knock sensor, still has code. BUT...engine runs to spec, OD works, mileage is off a little, 2-4 mpg lower on new engine, less than 500 miles...calls me up, says to drive it, mayber it'll clear itself...
this is also posted on YotaTech Forum as I'm looking for some insight

 

[SV_Dude]

If the knock sensor and the pigtail harness for that sensor were replaced then my guess would be something funny in the main engine wire harness. That would almost make sense as to why you're getting slightly less mileage too. I believe that any time the ECU throws a code the ECU goes into closed loop mode and runs on a default setting which is a little richer than what is needed in order to prevent the engine from running lean and burning up. I would suggest having your mechanic looking at a wiring diagram and chase the knock sensor wire in the main engine wiring harness. Also have him check out the grounds in the harness too. If the main harness was moved around while the engine was replaced maybe an old brittle wire was stressed a little more than it should have been and isn't giving a clean signal anymore?

 

[BigBoox]

Just getting back to this...Still have the KS code, but there still doesn't seem to be any issues with engine running at highway speeds(60-65MPH) on 31" tires although there is a 5 mph discrepancy in the speedo. Gas mileage, using the ethanol blend here in NY is around 16 - 16.5 MPG. engine timing, as checked by my regular mechanic is spot on at idle and highway speeds.
in the meantime I also contacted my cousin, a former Toyota Service manager and author of a software program for Toyota dealer ships, and inquired regarding the Check Engine light and lack of symptoms. His recommendation...put some tape over the light. While this seems a bit far-fetched I don't know what else to do. It does appear that while the code is showing, there are NO engine operating symptoms.
Thoughts, comments, concerns? Should I just leave well enough alone?

 

[91'4bee]

Try putting a different ECU in from a junkyard(cheapest). See what happens...