What is the best way to wire in the factory subwoofer behind passengers seat in the cubby there. I'm trying to wire it in on a car that doesn't have the existing wiring to suit.

Cheers in advance

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You'll need to run your own wires from the amp, I ran mine underneath the kick panel. Are you using the OEM woofer inside the box?
 
If you've replaced it (like you probably should), I cut the plug out of mine, bought a new plug from Jaycar and fitted it through the hole.

IMR22C
You'll need to run your own wires from the amp, I ran mine underneath the kick panel. Are you using the OEM woofer inside the box?
 
If you've replaced it (like you probably should), I cut the plug out of mine, bought a new plug from Jaycar and fitted it through the hole.

Will my mr2 have the amp in it as well or was it only used in the ones with upgraded audio

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What’s the best woofer to use in these? I have two boxes I want to install. But not with a 20yr old woofer!

Sw2091

IMR22C
You'll need to run your own wires from the amp, I ran mine underneath the kick panel. Are you using the OEM woofer inside the box?
 
If you've replaced it (like you probably should), I cut the plug out of mine, bought a new plug from Jaycar and fitted it through the hole.

Will my mr2 have the amp in it as well or was it only used in the ones with upgraded audio

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The OEM amp was only fitted to vehicles with Premium Audio. Your best bet is to buy a small amp and mount underneath one of the seats. You'll need to run all your own wiring and RCA's though.

mr2pete
What’s the best woofer to use in these? I have two boxes I want to install. But not with a 20yr old woofer!

I used a set of 5 1/4 inch Polk Audio subwoofers (Model MW5530) that are no longer available and are getting harder to find.
 
Most people use a brand called Tang Band. A fair bit of trimming is required to fit them within the OEM enclosure, which is what turned me off them. Good little subwoofer from all reports.

+1 for the Polk woofers.  I bought mine off eBay a few months ago and they sound great.  They dropped into the factory enclosure with no modifications except for crimping on spade terminals in place of the stock connector.  They won't blow your hair back and forth, but they're surprisingly robust!