Help Get a 3.2 running perfect, Hesitation and stumbling at 3500 rpms Options

[Heeltoe914]

Well after a hard few weeks of trying to get two cars ready for the GAF event we are happy to say we made it, both 914 3.2L conversation cars rolled out the door for some fun with others. It was great to meet up with so many new and old friends from the 914club and friends from my racing days with POC.
On one car we know the history and had run the motor so we know everything about it, the other was a purchase that not even the seller could give much info about the motor. But after hours of hard work we got both cars running and running pretty good, Except for one problem that leads me to this question.
On my friends car the injector had clogged or gummed up from setting and all 6 had to be changed out, this made it run and idel pretty good but at 3500 –4000 rpms under load it has a steady hesitation or miss. We have tried all of the following with new or known good parts with no success at fixing the problem. And when you come to a stop it will die if you don’t catch it by giving it a little gas. Up to 3500 or so it runs strong. After 4200 rpms it run good. Turn the key let it sit it idels fine.

Changed ECU
Idel air meter
ECU relay
New fuel pump
Mass air flow meter
All wires checked about 3.5 ohms
New plugs cap and rotor.
Checked Grds and connection
Fuel pressure at 30-PSI average
Valve adj, done.
Changed out Coil

The next two items is the Throttle position sensor, and the Reference sensor.
Question; On the flywheel from Kennedy Engineering When the pulley & rotor are pointing to TDC the single pin that the Reference Sensor reads is about Two inches over from TDC, Should this matter?
Any tips from you guys on fixing the hesitation would help out. Thanks for the time.