Replacing 300 gallons of water of a 3700 gallon total is quite a bit of water, and it's no surprise that your CYA has diminished...especially when you add in water lost due to splashout, backwashing, etc. However, check your owner's manual for the SWCG unit-they normally recommend the CYA level that your unit will operate best at--and that recommendation is designed to help the unit work at its most efficient and make the cell last as long as possible. With your CYA that low, you're over-working the unit (or underchlorinating your pool).
You do need to get the pH up, and depending on how low it actually is, that can be critical, especially if you have a heater or vinyl liner. We recommend Borax for that purpose. Sorry I can't help you with the pool cover question, but I'm sure someone will be along shortly that can offer you some advice on that.
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