Re-reading your posts, I noticed you said the engine has 044 heads. I don't think CB Perf. ever equipped those heads with stock (35x32 mm) valves, so this leads me to believe that the engine has bigger valves. They are probably 40x35 mm, as Pat wouldn't put heads with 42x37 mm valves on a 1776 unless the thing was cammed to make power somewhere above 7500 or 8,000 rpm. With 40x35 mm valves, again, this leads me to believe that the engine is set up to make power to 5500 or 6,000 rpm, which means the exhaust on it is definitely too small and it needs 1 1/2" primaries (the tubing coming off the heads). I'm doing a lot of assuming here, as there's no information about what's actually in this engine. It's easier to upgrade when you know what's in the thing (valve sizes, porting, camshaft, and compression would be nice too!). I'm not criticizing, as this is all the info you have, but only pointing out how this would be easier if we had the proper information.
A couple of questions- how high did it rev with power before you put the bigger pistons and cylinders and 1.25 rockers on it? Would it go to 5,000 rpm? Higher? When you bolted on the rockers did you check geometry at all (you use an adjustable pushrod) or just bolt them on with the pushrods you had? The reason I'm asking the last question- if the rocker geometry is wrong the engine may not be getting all the valve lift it should be (it might not even be getting as much lift as with the 1.1-1 rockers you took off, although this is a very extreme case) and may be contributing to the problem as well. Any engine with dual carbs (even with a stock camshaft and stock rockers) should rev to 4500 or so with power, so you saying that it "tops out at 4k" is raising a little bit of a red flag here.