yea it deff sounds like the wiring harness was might have a loose connection. also over time teh internal amp on the deck tends to go. If u do decide to go with a upgraded head unit these are some things u will need a install kit and a wire harness.
Personnally i put a rediculous sterio in my tracker. they are good for getting high decibles cause they are small. with a hard top u can reach an even higher spl (sound presure level). Ive got two Rockford Fosgate 10 in hx2 1000 watt peak subs in a custom down firing box, a pioneer mpv-840 dual screen head unit, jbl gto power series 4 inch speakers, an mtx thunder amp for the internal speakers, a rockford fosgate 1501db 1500 watt rms amp for the subs, a 2.5 farad cap, a lightning audio 950 amp battery. Also i have a viper paging system alarm with remote start, best thing no more cold zuk in teh winter
Unfortunantly i still have a soft top, with the subs it baloons out. if any one has any car audio,video,or alarm questions just ask