Actually before attempting to change the kickdown cable settings or worrying any more about the transmission's behavior, I would look again at the settings of the injection pump.
Based on the fact that we now know the engine is down on power, which we had not understood before when you first mentioned the transmission acting differently, I believe what you are noticing may not be related to the trans at all.
Lack of engine power (or changes in engine power curve) can sometimes confuse the driver into believing there is a transmission issue when in reality there is not. Since you have to push further into the pedal to get the power you need out of a doggy engine, it affects the transmission shift points/quality and can fool you into thinking the trans is acting up, when in reality it is only doing what you are asking of it with your foot, and the engine's misbehavior is the issue instead.
I once knew a guy who had an automatic transmission REBUILT at huge effort and expense in his TDI car because he believed it was "slipping" -- engine revved high with pedal to floor but car did not accelerate -- when in reality, the only issue was that the engine had a clogged fuel filter.
The trans would kick down since the pedal was floored but the engine had no power at high revs so it acted just like a slipping gearbox, at least in his perception. Point is you have to be keen in your observations about what exactly the drivetrain is doing to catch subtle differences in symptoms and go in the right direction for a solution.
My recommendation for now would be to IGNORE the different behavior of the trans and FOCUS instead on why the engine seems to be down on power. From what you are saying, it sounds like it has a lot of lag and very soft power when initially starting out, but then once engine speed and turbo boost comes up it is OK. This can be a sign of the "smoke screw" (fueling quantity adjustment screw) on the IP not being turned in far enough. This gets changed when the throttle controls of the pump are being worked on, which is exactly what recently occurred on your engine. They may not have gotten the screw back in the right position.
Two questions to answer:
1) If you floor the accelerator taking off from a stop, do you see a puff of smoke from the exhaust? And does the car feel as strong launching as it used to?
2) Are you familiar with the "smoke screw" on the pump and its location? Would you be comfortable making some adjustments to it, if we give you guidance?
If the answer to 2 above is "no" then the best plan is probably to bring it back once more to the folks who did the work on the pump for you, and inform them that they may need to recheck the setting of the fuel quantity screw since the engine is down on power.
ALSO, when was the last time the fuel filter was replaced? And you are not seeing any air anymore in the inlet line from the filter to the injection pump, correct?