Im currently doing a b20 swap on my 00 civic. It starts and runs, but i have problems with overheating and my first gear goes up to 45 mph (manuel) and also my shifter falls through. Any suggestions would be appriciated

 

overheating:
did you install a new thermostat?
is your coolant properly bled?
i realized when i installed a b20 in my integra that some obd2 motors don't have a bleed valve at the upper radiator hose. so, you have to be very careful to get all the air out of your system. not sure why honda decided to make this change.

there are many reasons for your motor to overheat and they would include the same basic components, regardless of car make - water pump, radiator, thermostat (as mentioned above), radiator fan, coolant, etc. i'm assuming the motor is in good health.

i don't understand the comment about first gear going up to 45. is it an automatic and the transmission is waiting too long to shift? if so, check to make sure you have enough atf.

shift boot?