A few things come to mind, check the fireing order of the plugs and check for correct gasket under the carburater! The HEI should make it idle better no matter what the engine condition is, internal problems won't become worse with better ignition. Double check the plugs, make sure you didn't crack the insulation putting one in or bump the gap closed.

I like to set the timing where it idles the best with out the vacuum advance hooked up. Lock it down, hook up the advance to full vacuum and adjust the idle speed at the carburater. With the low compression and better fuels now, you can get away with more timing then the factory settings. You may find the mechanical advance of the new HEI is a lot differnt from your points set up. The timing at idle is not nearly as important as the timing at cruize speeds so I set the timing at high rpm (approx. 2500 rpm or where the full mechanical advance is in) at 34*. I don't know where the idle timing is set, I never check it there because it doesn't matter that much.
Once you are happy with the timing, move on to the carburater. It sounds like the jetting is wrong or the gasket under it is blocking the vacuum ports. Check the gasket first, make sure the open port lines up with the slotted gasket. Next, pull the top off and check the jet size and rod part number and compare to the old unit you pulled off. Check float level and float drop measurement. These are all simple to do and will help verify all is right for your application. The idle mixture screw is for idle only! It should be set for maximum rpm/vacuum at idle. Set the idle speed using the throttle lever set screw, then set the idle mixture screw ( start at two turns out from fully closed), alternating between the two till the correct speed is set, somewhere around 650 to 700 rpm. A very slight hesitation can be overcome using the idle screw, but only a very slight one. Just a touch on the rich side, say half a turn out from ideal idle speed, anymore then that and you are waisting fuel and fouling plugs.

Yours just sounds like its jetted to lean, check out the two and let us know what you find. A vacuum leak can also cause a bog and now power. Joe