The issue with a Stanadyne pump wanting to stall when dropping from high speed is usually from a sticking metering valve. Try running either DK or Stanadyne lubricity formula through it and the problem should go away.

 

Filling an empty filter with Diesel Kleen will not hurt an IDI IP.
And it will start just fine.
It will idle a little funny for 30 seconds or so, but the that is just the rest of the air working through the system.

Back in the old days I used ATF, but addatives like Diesel Kleen were not as available as they are today.

Consider a quart of ATF will treat a tank of fuel.
A quart of Diesel Kleen will treat 300 gallons.
So for regular use, Diesel Kleen is cheaper than ATF.

Using a strong concentration like filling the filter with Diesel Kleen does cost more, but it also will clean and lubricate the IP better than ATF will.