Now we are concerned that some rocks may change the PH of a pond or not be fish friendly. I believe this is the case with limestone. Do you know any rocks that are not compatible with koi ponds, are which are the best choices.

First, do a biotest with any rocks you're not sure about.

A biological test is essentially a test on living organisms in a smaller, isolated system before applying any treatment to the main populations. This will help determine the exact safety of a drug, ornamentation or modification before placing all the livestock at risk. An ideal situation is found in establishing a smaller, perhaps 10 gallon system, with parent-tank water and adequate heat and some aeration. Conditions should be roughly equal to those of the parent system. Fishes should be selected for the Biological test that are of concern in the main system, for example, if goldfish are a safety priority, one of these should definitely be in the bio test system.

The bio test runs for at least 12 to 24 hours before anything is done or added to the parent-system.

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Rocks that raise pH are DESIRABLE in most areas. If your tap water has a low KH then limestone would be ideal. If your regional tap water has a high KH or GH then limestone can cause some problems. Always keep the KH under 350 ppm -

The only rock I know right off the bat which's toxic is OIL SHALE - it will leach petroleum into the environment slowly over time.