Mach 460 Help Needed

Been searchin and cant seem to find answer. I have a 2002 Mustang Roush Stage2 convertible with the Mach460 sound system. The head has the internal 6 disc changer, 2 amps next to the tops pump behind rear seat (ck'd connectors), and dont/didn't know about an amp under dash til reading thru forums. (Suspect thats maybe the Mach1000, dunno??). Id left it parked for an "extended time" and let the very OLD battery die. After replacing it, now the only thing on the heads display is the clock, other than when loading/ejecting... CD's will load and eject, but other than that nothing will come on (for the Mach system). Before it was parked, on rare occasions it would get noise thru spkrs like a fairly loud popping while driving or started, with sys turned on or off, if i recall correctly. Sounded like maybe something from alternator noise or maybe a bad ground?? but again, this was rare, maybe only 2-3 times and would always go away within a day. When I'd parked it, the stereo was working fine. As I write this, I'm thinking the "theft" light (PATS sys) on the dash does blink now with car started too, I'll have to verify that and repost an update. My wife lost her key, so now we only have one in case theres a reset needed requiring both keys, guess I'll need to get that. Ive pulled the head out and verified connectors and took pics of all the ID tags on the head unit in case theres some reset procedure from dead batt/theft issue with the PATS system causing my prob?? I can't find ANYTHING on how to do a reset, or if theres even a procedure for that? Bought the car in '04 (it had ONLY 4K mi's, YES!!!) and didn't get the car owners manual. Have tried to find fuse layout and schematics and not been too successful, but I have instead checked all fuses under dash and under hood, all good...least i think ALL??
ANY IDEAS, HELP, ADVICE, GUIDANCE in troubleshooting this issue will be greatly appreciated. We are about to prep it to sell. Had nearly thought to just replace the 460 w/aftermkt head, but sounds like more pain that I really want. I'm capable of job, no prob, just not THAT interested if it's not simple as JUST getting a better head with harness adapter plug, to play, & forget it.... if we're not keeping it anyway. Would rather fix this one, even tho, agreed, the Mach system IS junky to me when compared to what "they" think of it & whats available. ...and... it was good enuf for her too, LOL.
THANKS A MIL for any help, sorry so long, but tried to be clear on all I could. Dont know where to turn??

Tommy & Dee B
Louisville, KY
tdb921@hotmail.com