First, I think Chris Harris' comment on valves was regarding the 4 valve engines.
Have you checked the throttle position switch, that may have some effect.
Throttle air screws are set to 1 1/2 to 2 turns from bottom. I set the last one that has the vacuum line for the pressure regulator for 1 1/2 and balance the others to it.
Did you have the injectors cleaned? If they are gummed up with old fuel, they might not work well at small throttle openings. If you haven't had them cleaned, get some Techron fuel system cleaner and run a half bottle through each of two tanks of no corn gas if you can find it. A little YeeHaa will help loosen things up.
Last, check the timing of the Hall sensors. It's unlikely to be off, but you never know. No need for a timing light. There is a cutout in the mounting plate that lines up with the case when they are in the right spot. The factory manual has a nice photo of how they should look.