There's not very much you can do:
-The capacitor value is good, but it needs to be another type: Panasonic UF series are know to be one of the best, I'm using this one also, not cheap.
- The pins are bend and you can't correct if not done properly.
- The WSR2 is far too large, it can't replace the existing ones.
- you could change the resistor on the alert pin to a higher value (3K9 or 4K7) but bringing it out to the Estop will require major changes to obtain a reliable configuration.
- The diodes on the my THB6064 design didn't have much effect, this chip is similar so I don't think you will gain much, maybe a few degrees temperature reduction, not worthwhile to install them.

I would replace the cap and change or remove the alert resistor and try the drive with conservative settings and see how it goes.