Formatting your needs in a better way. Because it is difficult to understand your current setup. Do clear what all you have now, what you want, what type of music you listen to, and your budget for the install.
As far as I could understand, your Current ICE:
-Stock HU (without any preouts for connecting amplifier)
-2 Front Coax (on the door)
-2 Rear (Oval?) Coax (on the boot door)
My advice would be to upgrade in stages, less hassles and less funding required at a point of time. Stage 1.
Get a decent set of front components. Hertz, Infinity, Polk, JBL, etc. make same good VFM
components and can be had from 5k/8k depending on the brand. The coaxial from the component set can be placed in the front doors only. The crossover can be placed somewhere inside the door panel and the tweeter can be fixed on the dashboard edges or the ORVM's inside area. Stage 2.
If you are not satisfied with the above setup, get JBL 6x9 Coaxials fixed on the boot door. These would help create fullness in the overall sound quality in the car. At this stage, you can get a 4 channel amplifier to power the components and the coaxials. The coaxials would cost you around 6k for a powerful setup from low-mid level manufacturers like JBL, Pioneer, etc. The amplifier would cost you 5k/6k for JBL, Pioneer, Kenwood, etc. My personal preference would be to get JBL. The wiring can be dependent on your budget and quality available. It would cost another 2k. For connecting the amplifier to the HU, you will have to get a Hi-Lo Converter or Choke to create preouts. Otherwise, if your amplifier has speaker level inputs, then there is no need to get a converter. I am using JBL converter and it came for around 2k. Stage 3.
If you are still not satisfied with the bass output, then you can upgrade. With the SQ, there is no way that you will not be satisfied if you pair a decent set of components with a decent amplifier. The 6x9 can be made to run directly from the HU. The remaining 2 channels of your existing amplifier can be used to power a subwoofer. The subwoofer would come in for 3k/4k for a normal 12" one from JBL, Pioneer, etc. I have used the JBL GTX1200 and was extremely satisfied with its output. It costed me 3k without b/w. The subwoofer can be placed in a sealed box custom-made to fit your Scorpio without eating up much space. The box will cost 1k and less. You can remove the subwoofer easily when you want more space at the rear. Stage 4.
If you are not a huge audiophile, then you'd be satisfied with this much. If not, you can fine tune your system by damping the doors and boot door. Damping sheets are available easily and would cost 5k/10k depending on the brand you choose. You can also look at options to upgrade the ICE components with which you are not satisfied at this stage. Plus, you can add another mono amplifier to power your subwoofer separately and the 4 channel amplifier can power all the speakers. The mono amplifier would come at around 8k.
Hope that helped. Clarify your budget and other details, so we can suggest better.