PMO's baseline jetting is just an educated estimate based on experience with what others have successfully installed. So it should be considered a starting point. Your engine's state of tune (outside of the carbs) and your driving conditions (street vs. track/race) will dictate where you want to be in terms of driveability. Without question the AFR is what you need to measure to dial it in properly. Get a wideband AFR gauge, an LM-1 or LM-2 meter or take it to a local dyno to dial it in.
Also note that the Weber jetting people have honed-in on successfully is a good guide but don't take it as gospel. I'm not trying to be difficult or stir things up. Just pointing that out because PMO, while very similar looking, is quite different due to the improvements PMO made to their carbs.
PMO main jets (both air correctors and fuel jets) and emulsion tubes are not the same as our Weber 40 series used on a typical Porsche flat six engine. The PMO hardware is same as the two barrel Weber 48 IDF series where the emulsion tube, air corrector and fuel jet are all in one stack. PMO chose this arrangement because he felt it is a better design that Weber used to put the components all in one chamber within the carb. PMO also uses the needle & seat & the float chamber design from the 48 IDF
Not to mention the PMO has adjustable/variable idle jet air correctors that also influence the mix. Like Lindy said, the idle jetting is not just there to manage pure idle conditions. Idle circuit jetting has a heavy influence on the air-fuel mixture all the way up to around 3000+ where the transition occurs to the main circuit. So up to the transition point (and above) the idle circuit is playing a role in the overall AFR.
Typical Weber emulsion tube number designations don't apply either. So don't get those confused, if you're not confused by my babbling already.....
Another thing worth noting, the PMO seems to need a LOT less accelerator pump volume/delivery than the Webers. The accel. pump delivers a shot of fuel into the carb throat when you move the throttle. It helps avoid hesitation between the time you apply the throttle and the time the carb takes to react when the actual throttle plate opens, which draws more air into the carb, which then pulls more fuel from the fuel bowl, to feed the engine more fuel and thereby make more power. Back to the original point..... You may find it worthwhile to reactivate the accel pump delivery. How did you close it, just disconnect the pump rod?
What happens with too much accel. pump delivery is it throws an overly-rich mixture into the combustion chamber and the engine bogs a bit due to the extra time it takes to burn that rich mix. You can see this on a dyno graph or AFR gauge very easily. When you floor the throttle to full GO, the accel pump squirts a big shot of fuel in there and that makes the AFR dip considerably. An example of that is this guy's dyno plot
3.0 to 3.2ss with pics and Dyno sheets before and after
Check out at 3000 rpm where the AFR dives to 10 momentarily. I think that's due to the accel pump delivery volume being too much. Typically you do a dyno run by bringing the car up to around 2500rpm in 3rd gear and then they mash the gas pedal and the accel pump squirts the extra fuel right then & there.
In your case, your difficulty getting it going until 2000-3000 may be the LACK of an extra shot of fuel? Just a guess.