Lots to unpack here.
1a) I'd have set his pitch count, in a 5-man rotation, at 65/70. If you pitch a guy when he is less than 100% on game day, you will increase his risk of both minor and major injury. This is true of all players; the lower their fatigue number, the greater the risk of injury.
1b) The degree to which his ratings return will depend on his makeup, and your training and/or medical budget.
2a) Stamina improves only in the offseason, and the only thing you can do to improve it is increase your training budget.
2b) About development in general-- you improve power, stamina, velocity, range, arm strength, and the yellow ratings only in the offseason and only via your training budget. You improve control, splits (hitting and pitching), GB/FB, pitches, glove, arm accuracy, pitch calling, contact, and batting eye during the season, and these things are improved by playing time and coaching quality. All of these things usually develop for 3-4 seasons (sometimes fewer, and usually fewer for internationals signed at an age greater than 18) and then only trickle forward after that.
2c) Recovery from injury is an exception to when things improve and what makes them improve. Diamond in the Rough status is an exception to how long players develop for; a DitR event basically gives a player a whole new baseline and development trajectory.