2000 Tundra glitch

Do you have the 6-speaker system (with the tweeters) or just the standard 4 speaker thing?  If you do have the system with the tweeters, then you also have to bypass the factory amplifier (don't worry it's actually really simple for most toyotas).  The wires with the plug that goes in to the back of the factory radio...well these wires should run about a foot or so to another bundle of wires and plugs.  Unplug the male end  from the female for each connector (should only be two connectors), then get yourself a toyota wiring harness from any car stereo shop/store.  It'll be a set of two male connectors--both are rectangular, but one of them is wider than the other one.  The bare wires go to your aftermarket radio, and the connector ends just plug in to the car, where you just had to unplug stuff from.  Sorry if this is a lil confusing but it's kind of hard to explain without a picture of some sort.

From the way you've described your problems I'm almost positive that hooking it up this way will fix everything.  Just to make sure we're both on the same page though, I'm assuming that the back of your factory radio has plugs that look something like this.  The other set of connectors that are part of the vehicle's wiring, that I told you to unplug....well those connectors should look more like this.  Lemme know if you need some more help with this, and good luck!