Was this happening before you re-jetted and changed the filter? If not, reverse your work and trace every step you took to get there. Obviously something was not put back correctly. I would also try putting the stock filter back on, you may have bought one that is too restrictive etc.
If it did this pre re-jetting, then I would try running with your fuel cap off, and replace all of your lines. You may have a clogged fuel cap line or a minuscule tear in your line somewhere.
I would use your ohm meter to check your plug wire and coil.
Engine hesitation, which is normally most apparent during acceleration, is a condition that often results from either abnormal fuel flow to an engine or abnormal electrical conduction to a vehicle's spark plugs. Bad spark plug wires, whether they degrade internally or develop cracks and breaks in their outer coverings that cause electrical interference, can cause an engine to hesitate if they disrupt the normal flow of electrical current traveling from a car's battery to the engine spark plugs.
