Simple depth measurement is about 3" in the well, and you have about 2" more from the plastic spacer. The problem here is that most subs you are mentioning are well above that.
If you noticed, my 2nd build uses Fi Audio SSD subs (specially made for tiny sealed boxes, incidentally.) These just BARELY fit in my fiberglass enclosure, but they did indeed raise the floor level about an 1.5 inches above stock. To mitigate this lift, I had the amp rack cover at a slight angle to lower the backside down to near stock height...so it would look believably stock when you opened the tailgate. You could feasibly do this to your build, but I encourage you to compromise a bit with your sub choice and make it up somewhere else. For instance, in the EQ tuning. Besides, most subs are simply amazing compared with what was available just a decade ago.
The Zapco amps are processors in their own right, so if you can afford to play with them, I would. If you can't, you can match their sound quality with ARC mini amps or perhaps JL's HD series. The PDX series are very nice as well, but some complain that they are "cold" and somewhat "digital" in sound quality. For the record, I am a firm believer that any modern solid-state amp sounds just fine*, but your ears may be more discerning.
For components, before you decide what you want you must first decide what type of sound you prefer. In other forums I have had excellent success with a simple form I have people fill in. With it, I get to peek inside your head for what musical style you are tuned in to. Here's the form, just fill it in to the best of your abilities:
I need to know your car, your max budget, your needs for space, and your musical listening preferences.
For car - I need the year, make, model, and trim that it comes with. If you already know what speakers it fits stock, that helps.
For budget - keep in mind a good system starts with a "big picture" point of view. Therefore, all systems will need various ancillaries that can't be avoided (deadening, wiring, etc.), so a COMPLETE from the ground up system sometimes runs higher then you might see advertisements for in your local paper. I can build something worthwhile as low as ~$550 or so, depending on the car. Keep in mind, there are significant advantages to raising your budget. More power, more clarity, better efficiency, less wasted space, more features, etc. all come into play. And with all things, you MUST PAY TO PLAY. Equipment from systems will probably outlast the car and might go into your next car or two, so keep in mind that it is an investment not just throw-away money.
Your needs for space - I value, above all else in systems I build, usable space left over. I think even the most powerful and showy system still deserves to be livable in a daily driver. If you are building a show car, my thread isn't for you, this is all about stealthy and hidden daily driver solutions, where possible.
Your musical preference - we all listen to different music and at differing volumes. A while back, I composed a list of "this or that" and a sliding spectrum between the polar opposites, and I'd like you to use it to help me figure out what you expect. Here's the list:
Laid Back - 1 2 3 4 5 - In your face
Detailed/Intricate - 1 2 3 4 5 - Smooth and blending/ambient
Loud - 1 2 3 4 5 - Subdued
Concert/Live sound - 1 2 3 4 5 - DJ/Premixed Sound (meaning, do you prefer your music live and natural, or more pre-recorded and boosted in some areas to accentuate the music?)
For the dollar, whatever that number might be:
Power/volume 1 2 3 4 5 Clarity/Detail
Next, tell me your favorite genres of music to go along with these scales.
Lastly, do you care about rear passengers and their sound? Yes/No
One more thing...If you have ANY audio gear now that you'd consider using, list it.
I've found with these essentials understood, I can usually provide some suggestions that will impress as a total package. GO!
Obviously I lifted that from my other threads, so we already know your car and other important info. But, complete the rest for me to patch some ideas together.
And, give serious consideration to the JL pancake subs if you are playing with brands like you've mentioned. Your budget sounds like it is nearly ideal for it...and the JL pancake is the ultimate flat-panel sub currently out. Stereo Integrity is working on a special one called the BM, but it is not ready yet!
* The point is that while one amp may sound different from another, the difference can be corrected with minimal EQ work.