With any single carb setup, including stock, there tends to be a problem with fuel staying atomized over the long trip to the heads. It condenses on the walls of the manifold, leaving the remaining mixture on the lean side. The condensed fuel eventually drips down into the engine, but it's in the form of droplets that are too large to fully burn in the time allotted. In a lightweight sandrail that's used mostly in the heat of summer there's not much of a problem, but it's a lousy setup for year-round operation in a heavier vehicle.
The factory provided exhaust heat to the intake manifold to reduce this effect, but most aftermarket manifolds offer little if any preheat. The larger the cross-section of the manifold the worse it gets, since flow velocity and vacuum are reduced - and here again most aftermarket manifolds are all wrong, with runners far too large for the job.
You're fighting an uphill battle trying to get smooth driveability with a center-mounted 2-bbl. As a rule the mixture will need to be made overly rich at idle and mid-range to cover up for the inherent problems of the arrangement. IDFs ship with F11 emulsion tubes; switching to smaller-diameter F7s allows more fuel present in the well which richens the mixture on initial acceleration, many have found that to be of some help. Redline offers a manifold that provides much better preheat than most, I'd consider that a prerequisite - but even with that manifold, getting enough exhaust flow from an aftermarket exhaust system is a problem. Where a stock muffler runs the preheat flow from one exhaust flange to a low-pressure point inside the muffler, almost all headers simply connect it between #2 & #4 exhaust flanges - that's better than nothing, but the heat transfers mostly by convection since there's no net flow. You need to plumb one end of the heatriser pipe to a low-pressure point (like the collector) in order to get any significant flow.