I'd still have a real starter/alternator shop test your alternator; might be the source of the rest of the noise.
The only aftermarket solution I've seen for the 88-94 radio control spot is a storage pocket, and there's a couple varieties of them. An old school one that has slots for cassette tapes (loose; not in their cases), another is just a simple pocket, and AMI makes one that has a lip at the bottom so stuff doesn't fly out when you mash the pedal. That one is my choice; holds most aftermarket stereo remotes without an issue, and room for a couple gauges if you wish.
AMI also makes the best dash kit for mounting an aftermarket (single DIN) stereo. It's slightly deeper than the other brands so they're less likely to bottom out before seating properly, and the colors are usually a better match.
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Richard