1994 Subaru Legacy Car running rough and backfiring

Hi,
Have a great old car, has been performing just fine. A few weeks ago, was diagnosed with an issue with the idle motor. The mechanic bonked it a bit, and suggested not to fix as it was an expensive item, and I'm in the market for another car. Problem also seemed to go away for the most part, except when first starting up. Since then, the car has been running a bit rough and backfiring here and there (mostly going uphill - live in the mountains). Today, the battery was completely dead first thing this am, for no reason apparent. We charged the battery, and the car ran better than ever for a 30 mile trip - idled beautifully, drove smoothly, no backfired. That is, until I stopped the car for an hour, restarted (barely), and limped home backfiring off an on the entire way, and running extremely rough, with very low power. Any ideas what could be happening? It's odd that whatever it is, appears to be off and on? We did try fuel injection cleaner a week or so ago, and are currently replacing the spark plugs.
Thanks so much for your time!
Judy Klautt