After my swap, I was having some issues initially. after driving, when i stop at a light or stop sign the temp gauge was going up to a little over halfway. when i began to accelerate again it went back down to below half.

So i let it cool overnight, opened the cap, filled it, bled it the best i could and with the temp control **** turned all the way cold, i let it idle. every 5 minutes the fans would kick on, and i would fill it with about another cup of water. i did this for at least 30 minutes until the radiator fluid stopped going down.

the gauge at that point would go only up to half or a little lower ONLY AT NIGHT when stopped and normal when driving, during the day it stayed about the same "normal" spot just below half

the last couple nights have gotten really cold, so i turned the heat on for the first time, now when im driving the temp gauge stays at halfway, even in the daytime, but at night, when driving less than 3k rpm, or stopped the temp will go to about 3/4 and stay there. i dont drive far so im not sure if it will go higher.

the fans work when ac is turned on, the thermostat was replaced last year, the top hose is hot, the bottom hose is cool, the radiator was replaced last winter, i had no cooling issues until i did my 5 speed swap. Which during that time i replaced the temp gauge sensor with an aftermarket from advance auto.

as said, before my 5 speed swap, i had no issues, the car was down for 3 days, right after the swap the problem started.

also before the swap my fans would turn on when i parked the car and turned it off, now the fans do not come on when i shut the car off

 

"So i let it cool overnight, opened the cap, filled it, bled it the best i could and with the temp control **** turned all the way cold,"

The temp control **** should be all the way to hot while purging the air from the cooling system. This purges the air from the heater core as well.

 

Did you use the air bleeder nipple to burp the system?

 

yes i did use the bleeder valve. but the problem was i couldnt close it while filling, so i just opened, filled, closed, then continued.

should i jack the front of the car up at an angle to bleed it?

 

Grab your fan blade and see if the shaft wiggles (you may want to d/c the connector for safety). The shaft bushing on my fan was completely worn into an oval, slowing the fan speed enough to let the temp creep up even at speed. It still turned. I couldn't figure out what was up until the fan motor started making a screeching noise one day. Changed the fan motor and she runs rock solid steady temp now. I buy the $35 cheap Chinese one and now I figure they last me about 2 years, but I put 40k a year on the car and lots of hot weather driving. Honda wanted $330 for the fan motor.

 

Not sure what you mean by this.

When refilling the cooling system, heater should be to full hot position, and the bleeder screw left open. Fill the cooling system while leaving the air bleed open. Only close it when a solid steady stream of coolant streams out of the nipple. If air or a broken stream of coolant is coming out of the air bleed, it still needs to be bled.