A good rule of thumb to go by when installing sound systems is to run your power wire and your signal cables on opposite sides, since the sginal cables (unless they are the more expensive ones) are NOT shielded, and will pick up stray electrical signals.
Here is a troubleshooting guide for you. Follow it and you will find your problem, or at least know what ISN'T.
First, switch the inputs on your amplifier...make your left input the right, and vice-versa. Now start your car and listen for that whine. Is it comming from the opposite speaker now? If it is, your amp is NOT to blame, and neither is your signal wiring from the amp to the speaker. Probable cause is the signal cable between HU and amp is too close to the battery feed cable. If the whine IS still present in the speaker it was in BEFORE, than your problem lies with the wiring between the amp and the speakers. You can only use this guide *if* you have a problem with just one speaker though. If you have noise comming from both speakers, use this to troubleshoot:
First, unplug your inputs from the stereo side and tape them up good so they wont pick up any stray electrical noise from the front end. Start the car...do you still have a whine in the speakers? If so, unplug the signal cables from the amp. Did the noise go away? If so, your cable is picking up stray noise...either get a better quality cable or relocate it. If not, there is a chance your amplifiers internal noise filter has gone bad, or perhaps a bad ground. I would try to find a better way to ground the amp first...I use 4 gauge with a heavy copper terminal (starter-type) crimped on, and not the cheesy cracker-jack rings you find in "installation" kits. Those suck.
Another rule of thumb too....twist your speaker wires. It is a proven fact that twisted wires reject noise better than non-twisted, especially if they are not shielded. This is why newer network cables and phone lines are twisted inside the sheath.
Hope this helps ya bud!
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