I didn’t miss any point, you weren’t terribly clear with what you were looking at / for / to do. Still aren’t being, but hey.
Speakers: from cheapest to expensive:
Eclipse makes some decent 2 and 3 way setups, the innovative thing is that the 3-ways mount like a 2-way, with a tweet / super-tweet. They also have some very inexpensive subs that sound quite decent, and some super-high-end stuff that is very value oriented price wise.
I like / have experience with JL’s mid-priced stuff (with the soft dome, I hated their aluminum tweeter) for components. JL’s subs are outstanding, but typically WAY over-priced, I’d check out Image Dynamics first.
I think Focal is pricey but worth it, IF you have a clean enough source and good amps. The titanium tweeter can be harsh if driven wrong / installed poorly / etc but it can also have excellent presence and the imaging is second to (little?) none. Their PolyGlass line seems to represent the best value, esp. if you like to turn it up, the higher-end Poly Kevlar line doesn’t do so well at higher volumes actually. Utopia BE stuff is un-reachable for most people, aka your 3k budget would barely get you speakers… Keep in mind this is JM Labs (french) we’re talking about.
Dynaudio makes some of THE best speakers I’ve heard. Period. I bought a set for my Z when I was huge into SQ and love them. They aren’t cheap but also aren’t horribly expensive - comparable to mid/higher Focal stuff. Notice that here’s a second line of speakers that is designed by a high-end home audio / hi-fi mfgr? Hmm… 
So there, I’ve presented my take on some stuff I do like.
Stuff I do NOT like:
Kicker - it’s just loud. MB Quart - omfg my ears are bleeding, horn-loaded tweeters DO NOT have a place in the car! Polk / Boston / Alpine / etc - I consider a so-so value at best, frankly, if you have the expendable income to spend on a car stereo, step up to something worth having if you are going to bother. Everything else is just noise
Head units / amps:
I can’t recommend anything BUT an eclipse head unit. I’ve owned such a variety of pieces from Kenwood to Alpine and Clarion to Sony and Pioneer Premiere, and there is NOTHING that has stacked up to the Eclipse for sound quality or interface design / ease of use (not so much figuring it out, but using while driving / not looking / etc). Their NAV units are better than any OEM one I’ve seen (for that matter, WORLDS ahead of the other aftermarket ones imo). The DACs they use in the cd player units sound fantastic, the time alignment is top-notch, and they are very unobtrusive sonically, with high enough voltage pre-outs (none of this “advertised” 5V crap like apline where it’s such low current it’s practically unusable).
Amp wise, Eclipse also actually makes some fantastic stuff and is pretty cheap - none of it is all that much power, but it’s CLEAN and the aesthetic is quite minimal too. JL actually is my preferred “value” leader - the “slash” series stuff aka 300/2 for front components is quite reasonably priced (imo) for it’s excellent power and mostly-transparent sound. Zapco’s “Reference” stuff is good, but mostly with certain brands of speakers - I like it with Focal, esp. bi-amped. They are typically somewhat more costly, and a bit under-powered though imo. My current favorite is Audison, but it comes at a STEEP price point - and is only worth it in a car w/ a fairly low noise floor (quiet exhaust, dynamat, etc).
So if I had to do your 3k job, I’d pick up a $500-700 Eclipse deck (CD5000/CD7000) a $3-500 2ch amp like the JL or Zapco, and a $500 sub amp like the 500/1 (or an eclipse 2/3/5 way and set it up with 2ch for fronts and the remainder powering the sub) and then buy some JL VR series components (soft dome FTW) and something like a 12W6v2 - it’s probably not worth paying more for speakers in a convertable. It’s up to you (obviously) re: box design, but I’d probably stick with sealed, that’s the nice thing about the 12W6 - it works in a nice small box like .7x cu-ft, sure “ideal” is bigger, but so what if you end up with a bit of an exaggerated 80-100hz, you NEED that in car w/ the top down! Spend the rest on good power distribution, some decent (basically, enough gauge, good copper) speaker wire, don’t cheap out on interconnects - in fact what I love about zapco is the balanced line drivers they include w/ the Ref. series amps - and some dynamat - not so much to cut out road noise but to dampen the doors / trunk (where you are installing speakers).
That’s my (more than) $0.02 - FWIW I still think someone should trust a 3k+ job to a shop, if anything for the sake of warranty - who do they call if you move? but hey, more power to you for doing it…