Our process is to prep the filler by running 180° water through the filler and lines for 1/2 hour, blow down with CO2 then cool with chilled deaerated water that has been run though a UV sterilizer.
Cleaning involves a recirculating caustic (only about .5%, we have been told that stronger solutions are hard on the soft parts and there is a pretty low soil load in the filler). This is followed by another hot water rinse.
Like you, we run all of these processes with bottles in place.
One thing we are doing that you don't mention is to run the hot water for sanitizing and the caustic through the buttons too. We installed a cam on the back side of the filler to actuate all the buttons while the bottles are in place. We have installed Tees in the gas lines that allow us to flush the solutions through the gas lines to just after the gas regulators (I also suggest putting check valves in above the regulators to avoid accidentally running caustic back into them if you don't get the valves closed). The tees lead to a bucket to collect the caustic. The vacuum line is disconnected from the pump and also feeds into the bucket. We dump the bucket back into the CIP reservoir by hand (for the hot water, we just run to the drain). This process effectively cleans and sanitizes the passages through the buttons as well.
We do not use any chemical sanitizers.
One thing we were recently told by a Cimec tech was that we should avoid running any of these hot solutions at over about 3 psig to avoid damage to seals.
So far, we have not had issues with counts from bottles using this technique.
Just out of curiosity, what is you average short fill count on an 800 case run?
Free State Brewing Co.