first of all holy ***** ! I'm glad you stuck with it. I just recently got my 68 thats set up pretty much like yours, 289, performer intake, and it took some ironing out.
I also had problems with hesitation, but my solution was fixed at the carb dimantle and re-assembly.
Other times it will idle at 2000, then after a minute, I'll tap the gas and it will drop down to 800 - 1000 and sometimes it will do okay when I put it in gear (night before last, it ran absolutely perfectly) and other times it will idle rough
ALthough I have a 570 holly, I'm assuming that your's also has a fast choke like mine, i push the gas, set the choke, let off of the gas and fire it up. Then when you hit the gas, its the norm for it to drop, but you should try to set your idle screw a little higher.
of course after i put in an inline fabric filter it ran fine (those holly's are to f'n touchy)
i think you said it somewhere, but just be sure your not sucking air between your carb and intake either.
I hope to god you get it running, mine also gets to 55 quick
although 3 days after i got it, i collapsed a lifter
(ran about 8k ...oops)
keep plugin away, your almost there!!!!!!