Recent problem with skipping

This is my first post. I have been customizing a P.T. Cruiser with the help of a far more knowledgable friend. Recently a problem arose. When I first turn on my vehicle, if I play a CD somewhat loudly, it skips. This only occurs for about 10-15 minutes, no matter what CD (Frequent with hip hop, rap, or similar beats).

The PT is brand new, so using the factory battery and alternator. Have 2 boss audio amps (1 for my speakers all pioneer 6x9s and components, 1 for my subwoofers (I believe 1000w and 1500w). I am running 2 JL audio 12' w6's with 750w going to each(I ran a 12gauge cable from my battery to the amp)..Recall friend saying 1.5 ohms?

Initially, my lights dimmed when I first installed the system. I installed a capacator, which seems to have alieviated that problem.

This issue with the skipping (only occurs on CDs, not with radio) just started up a few days ago (system ran fine for 3 months or so). I know when a vehicle is started, the battery expels a few volts and needs to recharge. Other electronics might not work to potential during this process. This was what a friend had pointed out to me, and kinda said I was S.O.L...

Any viable solution out there?

--Also as an aside, I have 2 kenwood 200watt 6x9s and 2 kenwood 150w 5 1/4 brand new speakers laying around as an old christmas present. I was thinking of adding them to my current system on top of what i already have. Could any one direct me to a decent site for adding these additional 4 on top of my existing (ill build a custom box or something) but I am not sure on dimensions (don`t think they need that large of an enclosure) or how I should wire them (heard in compitionions people have speakers for specific ranges). Would like to read up on this, even if I don`t add these (my next upgrade was going to be more speakers any how)

You need to ensure that the CD player is as firmly mounted as possible.  If it's allowed to move around a little bit, this can cause the skipping problem.  If it's cage mounted, make sure the tabs are bent tightly against the dash kit, and try adding a piece of backstrap to the back of the radio.

Boss does not make a quality product, so the power ratings are not going to be close to accurate (very inflated numbers).  (Consider an upgrade- no JL woofers deserve to be fed by a Boss amp.)  I wouldn't use 12 gauge to power an amplifier.  See what rating fuses are needed by the amp, and you can use the Power and Ground wire size calculators on this site to figure what size wire you need to use.  You can use 12 gauge to connect the subs to the amp, but don't use it for power.

While a capacitor may help to mask a light dimming problem, that is not it's intended use.  If you have a light dimming problem, then your alternator will likely need to be upgraded.  Otherwise, you can easily kill the factory alternator.

You state that the skipping has only recently started, but was fine for 3 months, which tells me the cage, or head unit mounts have probably worked themselves loose over time.

I don't like putting more than 2 pairs of speakers in any setup.  Choose the speakers you like, and stick with those.  While you "could" add those others, they will likely end up sounding horrible when combined with speakers of other brands in other locations, etc., etc. etc.

Thank you for your advice, so far my system has kicked the shhh out of anyone I have rolled up on in Vegas so far. The problem goes away after about 10-15 minutes of the car running though. I went ahead and checked the deck, it is secured tightly with a backstrap already.

What alternator or Amps would you sugest.

If that's a new deck, think about taking it back and explaining the situation.  When they see it's not due to an installation issue, they should swap it or send it off for warranty repairs.

As far as amps, go with a name brand- go to the stores and see what's available locally so you can give them a listen.  The alternator you select will depend on the amount of current your system takes.  Do a search on here (upper right hand corner) and you will find many different suppliers.