ALWAYS start at the basics first! If the engine is unknown to you internally (before now) then you'll need to establish a tune base line to work up from. Investigate any lifter or tappet noises first and get a cylinder compression check (find someone who knows how to do this and get them to either direct or do it for you). Check the manifold bolts are tight, the gap and condition of the spark plugs, rotor cap and button and condition and resistance of all leads, the carby float level is right and that the general condition of the all of the myriad of vaccuum lines in the engine bay are there and intact (and especially the temp controlled ported vac switch at the front on the drivers side) and not sucking any air. They also had a couple of issues with cam wear and fibre timing gears stripping so make sure what you have got is good.
Sounds like you may have more than one issue there. Holden sixes can tend to leak vac along the inlet manifold gasket and also the plastic vac tree/s rot away and suck air. Base gasket on the carby (check it again even though you have changed the carby already) are common and the bakelite plate underneath it needs to be in situ. Check the timing is actually set properly as the harmonic balancers are prone to slipping the outer ring (both around and/or completely off the rubber mounting) and if there is any evidence of the rubber mount starting to push out then replace the balancer immediately. The rubber often swells with oil residue around the engine and goes soft, allowing the outer ring to work its way off.
Check the EGR riser is free and that the valve butterflies are free to operate (depending upon the state the car was originally sold in), and that the stove pipe (the one from the exhaust shroud to the Thermac valve on the aircleaner) is refitted for cold (choke) operation.
The standard blue six is a great motor and they will run strong and well for a very long time if well looked after. One thing though, the engine will run smoother, stronger (yes, more midrange power and torque!!!) and use less fuel if you put the Varijet carby back on it - after getting it stripped down, checked and a kit put through it properly. Some will disagree (Rob, engarde!!), but is it really worth the defect notice to strip the emissions controls from it?
On the other hand, the Varijet soon gets out of its depth if you start porting, cam, raising the compression etc. The reason they work so well on the standard engine is that they work to keep the airspeed (not flow which is totally different) through the carby high, which increases fuel atomisation and engine midrange torque.
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