I highly recommend you read the
Signal Analysis FAQ that's linked to on your report. You will likely come to the same conclusions that I have.
First, you must pay attention to the "Real Channel" column, as those are the channels actually being broadcast on. The "Virtual Channel" is what you use to tell your receiver where to tune, and it is just a label embedded in the data transmitted.
Next, your report predicts exactly the results you are getting for reception of the Indianapolis stations. The two stations you have trouble with are a) weaker and b) broadcast on high-VHF channels. Your antenna is designed to be a UHF antenna, but it does have some sensitivity to VHF channels. The difference between the NBC and CBS channels is the difference in how the ClearStream 4 performs.
For the Louisville stations, your report correctly shows that you will have trouble with ABC, as it is again a) weaker, and b) on high-VHF. The report also suggests why you are having trouble with the FOX station. It is transmitted on channel 49, right next to a very strong CW station (WTTV) broadcast on channel 48.
You need to add a high-VHF antenna to your system, like an AntennaCraft Y5-7-13. Combine it to your CS4 with a special, but not expensive, combiner known as a UVSJ. Aim them towards the market of your choice.
There's no good way to combine an additional antenna in order to have both markets at the same time. If you want to have both, then get something like a Winegard HD-7696P and run a separate cable down to the TV. Use an A/B switch to choose which antenna system to use.