Hyundai Elantra 2006. A/C, Fan , Stereo clock not working after a poor jump start.

Hyundai Elantra 2006. A/C, Fan , Stereo clock not working after a poor jump start. Battery light started glowing. I took it to autozone and charged the battery up. they diagnosed the battery and alternator and suggested me to change the alternator. I have changed the alternator now and also have changed the fuse. Now all gauges in the dash spiked up initially and settle down to its normal after the engine ignites. Still the A/C, Fan , Stereo, keyless entry and Clock not working.

Please advise what could be the possible reason to fix and how much it would cost to fix.