Your koi appears to be suffering from either a bacterial or viral condition. If the white bumps would have given the fish the appearance of being sprikled by salt then the diagnosis would have been the Ick parasite but these are bumps and not as many as would appear had it been Ick.
The first thing that should be done is to test the water for levels of ammonia, nitrites and nitrates. Results should indicate ammonia and nitrites=-0- and nitrates 20 ppm or lower.
Testing is always the best first step because many fish ailments arise as a result of unfavorable water conditions. If you don't have a test kit handy then a water sample can be brought to your local pond store where they will usually test for free. I don't suspect a water quality problem but it should always be ruled out first.
After testing the water and confirming it's ok add some pond salt, see link below for example. The pond salt will serve as a general tonic and fights off many toxins. Just follow the directions on the product label for dosage.
Once the water has been tested and the pond salt added begin treating the pond with a medicine called Tetra Pond Pond Fish Treatment, see link below. It's desigend to treat a variety of ailments and will not harm the other pond inhabitants.
If the bumps are viral in nature then the Tetra treatment will be inert but if they're bacterial in nature both the Tetra treatment and salt should effect a cure. There are no viral medications available to treat fish. Many viruses will go away on their own as is the case with humans. Also it's possible that the stress of the pond repair is causing this reaction in the Koi.
As for the Koi hitting the gate when it jumps, yes this could hurt the fish particularily it's outer slime coat which is a fish's first natural line of defense. I would recommend placing a net over the pond instead of a gate as the impact would be lessened.
The best way to avoid stress would be to try and shield the part of the pond that the fish are inhabiting. I know this might be difficult to accomplish but the movement, vibrations and unpredictibility of the repairs will continue to stress them thus lowering their immune system making it easier for them to succumb to disease.
Best wishes and please let me know if you have any questions.