I replaced my entire system (well, head unit and speakers) but left the stock door subs and amp and they seem to do pretty damn well for what they are as long as I don't crank the bass WAY up. With the stock head unit they sucked but I'm fairly certain that's because ford set the cutoff frequency WAY too high.
I used the 12V to 5V regulator and ford adapter harness to wire the aftermarket head unit into the factory amp and set the low pass cutoff frequency to something reasonable. Now that I've done that the stock door subs sound a hell of a lot better than they ever did with the stock HU and hit a lot harder since the amp is only amplifying low range frequencies (and the speakers are only playing bass).
Rather than spending the money on new subs and/or an amp from the get-go I'd recommend trying to figure out which RCA/turnon wires controlled the OEM amp and hook your head unit up to the stock amp/subs and seeing what you think. It's far cheaper than just throwing parts at it... I mean, I had every intent to replace the door amp and speakers but found that the stockers are good enough for now. Sure I'll be replacing them eventually but that upgrade has moved pretty far down my to-do list.
For reference the factory head unit (shaker 500 at least) had 2 connectors on the back IIRC. One had wires for all of the speakers and such. The 2nd (smaller) connector had the subwoofer signals in it. If you can pick up the wiring harness for the shaker system it should have a harness adapter that adapts that connector to one with a couple RCA cables and the necessary amp turn-on wires.
Pretty sure this is the harness that I used with my Shaker 500: http://www.amazon.com/Metra-70-5521-...wiring+harness
Looked up the shaker 1000 system on crutchfield and it listed the same harness for the shaker 1000 system so that might work for you... (http://www.crutchfield.com/p_1207055...e-Harness.html
2005 Windveil Blue GT (MT)
93H Bama tune, JLT Series 3 CAI, FRPP CMDPs, Pype bomb super system, 3.73 gears, Steeda shift bushings, Saleen short shift block
Steeda ultralite springs, Tokiko D-specs, J&M Extreme joint UCA/LCAs, PHB, C/C plates, bumpsteer kit, Steeda Q1S wheels, 2011 GT brakes, 275/40R18 Sumi HTR Ziii tires