I think the rain might have broke my ebike

You don't say if you are running LiFePO4 or SLA.
I had similar issues with two ebikes..
The factory Currie 250w hub motor bike has a push on / push off button (and pas/tag) on
the handle bars.. Water in that will make it do strange things, inc refuse to turn off or on.
My converted SLA bike with 45A BMS and 40ah LiFePO4 got some water into the BMS and
I am pretty sure the balance circuit saw a drain across a few points and refused to enable output to the PWM.
Rinse with isopropyl, denatured is no better or worse, just messed up so you can't drink it.
The higher % iso you can get is better. Air or rice dry and try then.
I would discon the on/off sw etc and try via a jumper wire to turn bike on (if it's a soft
sw like my hub motor bike)

Drying it out wont help if a short caused a part to burn out. You got a new controller and now its fixed. good deal. Hope your new one is waterproof..

In my case, both bikes came back after drying out. If there were/are deposits on the board, then flushing it _MAY_ help. My post was more about waterproofing than anything else.

It is not the water that kill the controller, but the shorting.
When water gets into the controller, it is short circuiting the controller. If you try to use it when shorting, some components in the controller will burn and will never work again even if you dry it out.
Also, if you leave water inside, you will eventually see some green stuff on the PCB. Those are rust, on copper.
It is ok to leave the throttle on the outside as it is its normal design. It should be water proof. However, it is a bad idea to leave the controller outside.
The extreme heat from sun can melt the solder joint and as a result you have cold soldering. Also, try to insulate the controller from vibration.
Wiring is the tricky part. You should cover all the wiring to avoid something cut it by accident. When the power is cut and shorting to the frame of the bicycle, you are going to have some serious problem.
Watch out for the connection point on the whole circuit to make it water proof.
Finally, you can only test how waterproof your DIY is in the rain.

I keep all my controller, batteries, switches inside a trunk on rear rack.