There's a fan switch in the nozzle where the UPPER radiator hose attaches to the head. That one is responsible for switching the fan just after turning off the engine.

Run the engine for a little bit after a cold start. Not long enough to actually warm up the engine. When you shut it off, does the fan run? Unplug that fan switch in the upper radiator hose. Does the fan stop? If so, then it's probably a bad switch.

If that doesn't make the fan stop, then I'd suspect the fan-timer-module. It's located somewhere under the dashboard, but I never owned a 5th-gen so I'm not sure exactly where.

 

I will try this this morning and report back. Thank you for the help.

 

Yes there is def a problem.
I am going to start a new thread as making it its own thread will make it easier for users in the future to find it using search if they are having the same problem.

 

A little update

Today I pulled the car to the scrap yard and got $342 for it.

So my total costs for the swap are as follows.

$250 For the Honda with a blown motor
$100 for delivery to my home
$40 for clutch friction plate
$15 for Cone Air Filter (there was an aftermarket intake on the donor car)
$17 for front motor mount
$40 for 5 speed ECU

$452 total expenses
$342 Scrapped car

$110 total cost for 5 speed Swap

 

I forgot to add in that I sold the ECu for $20 so that makes the total cost $90 for the swap

I also have the taillights which are in good shape that I should get $30 for and the ECU from my Auto which I should get at least another $20 for

That will put me at less then $50 for the 5 speed swap

Plus I got a ton of spare parts from the donor car before I scrapped it.

Main Relay
A/C Controls
Dist & Coil
Power Steering Pump
Switches
Inside door handles
engine sensors
other misc stuff

 

Nice job. But you forgot a couple big things in your accounting.

Labor rate for your time doing the work.

Educational value (or entertainment) you got out of doing the work.

 

Don't forget the frustration factor!