Tee hee hee. When I started reading your thread, this is what came to my mind: "This turned out to be a bigger job than expected. "
Rocks on the bottom of a pond are a BIG debateable subject. We have discussed it many times here. Many professionals discourage it, for the very reasons you encountered - muck, gunk, and dangerous, oxygen-depriving chemicals building up on the bottom of the pond. Others have been enjoying the esthetics of rocks on the bottom for years with no problems.
I, personally, do not have rocks, and prefer the ease with which I can drag a net along the bottom to scoop up fallen leaves and etc. It's slippery to walk on, though. I also am not draining and cleaning my pond this year; the first time in 20 years or so. There's really no reason to do so, unless you have an issue you are trying to rectify. It's very hard on the fish, too.
Be sure you have temporary aeration in your tank, while the fish are in temporary quarters. If they are there very long, they will need filtration, too.
Keep in mind that the temperature in an in-ground pond won't be the same as in an above-ground stock tank. That being said, by the time I was finished draining, cleaning, and refilling my pond in the past, the fish were usually in such bad shape that I threw them into the pond, regardless of temperature or water quality, just so they could get some oxygen.
Let us know how it goes.