[FiShNc]

One thing to avoid is throwing parts at it. Not saying you did; it's just obligatory to get that out up front.

Swaps can be tricky to diagnose because it isn't exactly one car or the other.

Start by checking for CEL codes. Which ECU are you using? Using the correct ECU will be pretty important for getting best performance from the vtec-e.

Then go through a tune up procedure checking for problems. It may be you've already covered that.

Since you just swapped the engine, is it safe to assume you have clean oil, PCV valve, and egr? Also timing belt is on correctly? Double check that. Timing belts on these Honda's can sometimes be easy to screw up.

Did you rebuild the engine before swapping? How do you know it's in good order?

Are you using genuine Honda parts? Sometimes you can get away with other stuff, but there are certain parts that you should just stick with Honda: distributor cap, rotor, wires, thermostat, O2 sensor, etc.

Finally, details. Divulge as many details as you can even if your not sure it's relevant. The more information you give, the easier it is for the experienced people here to help.

Edit: just though of one more thing. What transmission are you using? Selecting the right gearing for your engine can get you better mpgs. The jerking suggests this is not just a gearing issue though.