Around $1k to start, I don't get a whole lot a free time so I would rather build each part of the stage seperately. The biggest thing "missing" is mid lows. Not looking for anything crazy, but would like a 7 speaker set-up. The idea I have is 2 sets of 6 1/2 components, 2 mid range and 1 sub. I have a soundstream ref 500s I can drive either the 2 mids or the sub. Would like a fi sub but the q being 1500w rms is more than what I need.
i want to mount the small subs in the sailpanels, but only 6 1/2"s will fit.
Keep it simple. You don't need 7 speakers and you don't need subs in your sail panels

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Of the 1k I would spend as follows:
1. Bit ten dsp $400. This will integrate with your factory hu and will take speaker level inputs.
2. For speakers all you need is one set of components for the front stage and a sub adding more speakers is going to add to your issues and will be a step away from sq as I know it. Sell the Alpine and kicker 6x9, lets assume you get ~100-125 for them. Add another $300 to this you can gave a really wide choice for your front stage.
3. If you use your sub for the 20-60hz, then a $1000 sub is not going to sound 5 times better than a $200 one. Box size and power is more important moreso if you're using them in a narrow bandpass.
4. Spend $3-400 on your install. Sound deadening, secure install, proper placement etc.
Once you have the basics covered, good sound is about tuning the setup via your bit ten. Good sound is NOT plug and play, irrespective of the $$ you throw at it. Even if you want plug and play start with a pair of components and sub.
You mention you want more lower mid range. Lower mid range is 300~500, I think you mean you're missing lower mid bass which is the 70-125 range. If the upper mids and highs are too bright in your car, they will mask out a ton of your lower end. That's a tuning issue.