When I read your post you have need to have a few goes locking the PHY PLL to the clock. Then you power it off and back on and it's again unlocked. So do you need to repeat your process ? Have you got a 100MHz signal generator you can connect into the PHY ? To rule out the PC. The datasheet may also have a sequence for the PLL getting lock.

This is a really good idea. Use the sun to heat a large thermal mass (the water tank) and then the coil and pump circulating through it back to the hot tub makes a great heat exchanger.

A few thoughts, there is a lot of ringing on the signal. Do you know what the max freq that the timer can put out ? Your description sounds like it doesnt have enough bandwidth. Have you got a pull down resistor on the output pin or straight to the scope ?

Yes I see that now having re-read it. I've adjusted the answer accordingly..

You are isolated so don't need the opto, unless they are doing level shifting ?