Hey guys,
I have a '65 that I just replaced the heads on. When I got the engine back in everything seemed great. However, every now and again...when I first start her up and get going, she hesitates a bit when accelerating and will only seem to be getting fuel if I pump the pedal. Then I pull over and rev the engine for a second and it clears out the problem and runs fine. I'm assuming there is some kind of blockage in one of the jets in the carb? It is my daily driver and usually seems to happen after sitting for a day or so. Any help is appreciated.

Few things to consider:

Generally if you are pumping the accelerator as your means of getting fuel into the engine (to compensate for a lack of fuel), it tends to be a lack of 'vacuum' present at the carb to suck the fuel out from the jets. This could be a leak at the manifold, typically a non-blocked vacuum line in the manifold or carb, or could be a cracked rubber manifold boot (if dual carb). If it only seems to happen when the engine is cold, it could be the auto choke (as this closes to increase vacuum at the jets for cold start fuel enrichment.

by the sounds its only when you try to accelerate under load (as opposed to just revving on teh spot).

if you have trouble idling (stalling) and pumping fuel keeps it going and vac wasn't an issue, then i'd inspect the idle jet. main jet shouldn't be the cause if you are 'accelerating' and thats when the hesitation kicks in from your description. Hesitation during acceleration can also be the result of the dreaded 009 distributor with the 34pict3 carb combo. Otherwise be sure the vacuum advance (if present on your distributor) is properly fitted to the carburettor. Distributor timing can also simulate a lack of fuel response too.

So.
1. Tell us whatengine, dissy and carb you are running.
2. inspect for vacuum leaks (check manifold boots, and manifold for unblocked vac pipes.) Can perform the 'spray aerosol around manifold to head joint and listen for revs to pick up, highlighting leak.
3. Does it occur when its cold?
4. Whats dissy timing set to?
5. Main and idle jets are easy to get to on stock carb. Blow em' out for security sake anyways.