I bought a 94 accord with a JDM H22a knowing it needed a timing belt replacement... After replacing the whole timing assembly/waterpump, it still hesitates... does it need a computer upgrade to run right?

 

A timing belt issue is a run or no run kind of issue, unless it has jumped a tooth.
A timing belt, be it old or new wont cause performance issues, until it breaks or jumps teeth.
Did you set ignition timing per the reference when you completed the timing belt?
What shape are your ignition system components in?
When does the hesitation occur, under load, throttle tip in?
Do you have any codes?

 

also, first thing in the morning when it is completely cold, the CEL is off and it seems to run fine, but as soon as it warms up the CEL comes on and it runs progressively worse throught the day

 

the hesitation is under load

 

Pull the code.