Hi konst-72,
Welcome to the forum.
The clock generator chip is I2C programmable and the two clock outputs are used for different tasks in the FPGA. There is a channel that is used for the main clock and that is fixed at, if not mistaken, 50MHz, and the other channel is used for the sampling clock of the arbitrary waveform generator. It is set by the software up to a maximum of 200MHz.
Just replace the chip with a new one and the configuration is taken care of by the firmware.
The FPGA can be replaced and will get its configuration from the second FLASH chip that can be found in the 1014D. No need to use the JTAG interface. Best to make sure the FLASH chips are also good and the data within them is still valid. As there possibly are versions that use a different FPGA then the one I have, it is best to post the type tag of it here and ask if any one has the proper FLASH content for it.
Mine has the Anlogic AL3-10 in it, and the FLASH contents is attached below. (Remove the .txt extension)