Cooling issues

If anyone has any idea what I missed here. First off I have an 03 Freightliner Classic with the 500MBN cat and a 13 speed behind it. The first mods I did were the fuel temp mod and a air pressure regulator, which worked great so I went on to a flash on my ECM I put it a 6NZ 550 horse flash and removed the air pressure regulator. Which is pretty good so far except for the turbo and exhaust which I am changing as soon as I figure out wht went wrong here lol. So I'm not sure if it's coincidence or not but round the time of the flash my fan quit working on auto. Manual works fine but left to its own it will over heat. I've changed all the sensors including the electric over air solenoid, I've checked all the wiring for breaks or shorts.

I spoke to a friend who is a mechanic at another shop and he's run into similar problems, he figured ECM issues were at fault so he bypassed it with a relay, always on temp switch and some creative wiring. I'm hoping I do not have to do this as I want to flash my ECM once more to a 600 horse 2k torque flash (by the way anyone have a part number for a this flash? 6NZ or 7CZ?) Im trying to do this in stages so I know what's working and what's not.

Ive lined up injectors and cam for this winters project on here, I'm hoping to get a Mr. Haney flash and PDI turbo and manifold as well as a few other changes. Just hoping to get past this current hiccup and keep moving forward.

Sorry this is a ill long winded but hoping to have all the facts there and hopefully someone will recognize a step I missed. Or possibly something I've done wrong. The old girl pulls 63,500kg's all day every day so I need to keep her cool. That's 139,700lbs south of the border