Upgrading stereo in 04 Expedition XLT

I just got a used 04 Expedition and I want to upgrade the audio system. Unfortunately, my options are limited because I want to keep the 6CD HU to control the stock DVD player. I have a JL Audio Stealthbox sub with 2-8" drivers that I took out of my 97 F150 before trading it in. I also have a Precision Power amp (300W RMS bridged) that I had used to drive the sub. Here's my question: I'm trying to figure out the best approach to upgrading my system, assuming I need to keep the stock HU. Obviously I need an amp and speakers, but I don't know if the stock HU has line outs. I'm assuming it doesn't, which means I need to use the speaker outs and either get an amp with speaker-level inputs or use converters to bring the speaker level signals down to line level. I'm leaning towards a 5-channel amp, like the Alpine MRV-F450 (4x60W + 1x200W RMS), instead of a 4-channel plus my existing sub amp. If I do get the Alpine, I can use 4-input mode to get the fader control (and because the back speakers turn off when the HU is in dual play mode, ie when playing a DVD). Will this work? Can I get a factory wiring harness so I don't have to cut existing speaker wire to set this up? I plan on using all new wiring, plus I'd prefer to keep the factory stuff reasonably intact so I can take the new gear out with relative ease if I need to. Also, regarding the sub. I looked into getting a Stealthbox for my Expy, but JL Audio says the version for the 03+ Expedition won't fit if you have AdvanceTrac traction control (because of the wiring under the AdvanceTrac disable switch in the center console). It so happens that I have AdvanceTrac. And I can't find any aftermarket sub enclosures that fit anywhere else (MTX Thunderform is only available for 97-02, and I'm not sure I would want one anyway; JL Audio sells a Stealthbox for the 97-03 Expedition, but it obviously won't fit). Right now, I'm just planning on throwing my F150 Stealthbox in the back, but it will take up a lot of room. Any ideas? I looked into getting the stock sub enclosure, then adding my own driver, but Ford wants something ridiculous like $250 for that. Any ideas? Sorry for the long post. TIA, Tom

"Here's my question: I'm trying to figure out the best approach to upgrading my system, assuming I need to keep the stock HU" You can remove the factory head unit and retain the use of the dvd player, but you would lose your steering wheel controls and rear seat audio controls. Mike