Marshall Smith - Apologies in the delay in responding back here, contract hours have been a little busy lately ! I did miss the embedded link you had in the original post and have seen it now! here's my thoughts;
1. You need component speakers for the front end. Spend as much as you can here as the performance of the front end is where you get the characteristics of sound quality, imaging and soundstage when mounted in a solid baffle. You've listed 'co-axials' so the tweeter in those if you installed them would play to your knee level and not to your ears. There's better brands out there and my recommendation would be to go for the entry or mid level ranges from dedicated car speaker audio brands such as, Focal, DLS, Hertz, Gladen, Morel, Ground Zero, Arc Audio H.A.T and similar (some of these also make amplifiers and processors as well). The reason is that it's less likely in the near future you'll want to change them in comparison to some 'usually' harsher/brighter sounding cheaper speakers. The issue is that cheaper brands often make their products with those characteristics which sound 'exciting' for a relative few minutes but quickly become 'fatiguing'. Not saying all are like that, but its a common aspect. Do look into well reviewed component setups from Alpine, Pioneer as well though, and of course with an eye on your price point.
2. For the rear, as it'll only be a bit of 'rear fill', you don't need to spend too much here, the ones you've shortlisted will suffice (check mounting depths though !) So overall, your spend split would be a 75-80% of your budget for the front and the remainder for the rear.
3. For the amplifiers, I'd take the JL Audio one and perhaps pair it with the 4 channel unit from the same range the JX400/4D. The 4 ohm rating for the JX500 is 300W RMS at 4 ohms, which is the usual benchmark. If you want to get the 500W RMS it's capable of, you can but keep in mind it'll run hotter so you'll need to take cooling into consideration. You'll also need to get 2 ohm capable subwoofer driver(s) too. The 4 channel JX400 is rated at 70W RMS per channel at 4 ohms. In my car, I'm running 1x300W for my sub and 4X75W RMS for my cabin speakers. It's plenty of power and if you choose your sub well along with it's enclosure, inside the car you can get awesome performance levels and yet outside the car, even with windows down, there'll not be a lot of sound or bass leakage i.e the common misconception that you'll be heard from the next block or want to make paving slabs bounce!.
4. Similar to the above, get a high quality and capable subwoofer, a good solid enclosure like in the above example and you'll get smooth, rich, controlled, musical, tight sub bass. With a nice setup session of your amplifiers gain levels etc, you can get a very nicely 'balanced' setup.
5. The Sony head unit is a nicely priced and well featured unit for sure. That single rotary control knob looks a little out of place and especially when in an E39 cabin as 'everyone' want the look of the oem 16:9 monitor! If it doesn't bother you then do shortlist it. Else, perhaps pickup an Alpine iLX-007 ? the great thing about these units are that it has higher end features like Digital Time Correction and a Parametric Equalizer built in. These kinds of features usually are on stand alone processors and cost more than the head unit itself! Add to that Alpine Sound Quality, it's a fantastic sounding unit. This assumes you have a iPhone as it'll only work with one due to being Apple CarPlay only. Do look at the other Alpine units iLX-107 and 207s.
6. Of the two subwoofer solutions you specify the better design is the GAS enclosure. Not sure if they're still around as a couple years ago they weren't doing so well and there's bit of nasty history with how they dealt with customers especially with the fiasco that was there E39 crossover unit. Also, technology has moved on, that enclosure is pretty much the width of the boot/trunk. Some subwoofers will perform in much much smaller sealed enclosures. I use the 8W3 V3 and have a look at how much smaller my enclosure is in comparison;
(Excuse Akita fur!)
You can see that the enclosure is perhaps 12 inches wide, 5 inches in depth and around 15/16 inches in height. To give you an idea of how it sounds, I've asked many enthusiasts and friends at car shows and local meets etc to listen and guess the size of the subwoofer they're hearing. Perhaps 65% said a 12", 25% said a 10"
and amazingly 10% or so said it was a 15" ! When I'd pop open the trunk/bootlid they'd look around firstly to see 'wheres the big sub box?' and then look in total astonishment at the piddly little 8 inch subwoofer !! There then usually followed lots of words mixed in with expletives too!
7. I've not seen those $34 baffles before! they do look good and will absolutely do the trick to provide your front components having a solid baffle to play from!
8. Alot of owners will 'automatically' assume they want 6.5's in the front doors. You can of course go for it, but it's more work to get right - see my initial post above.
Feel free to PM me and discuss any more aspects or questions and I'll do my best to help!
C4Racer - Drop me a PM! I can sort you out with our last PM/discussion
Josiahg52 - There are a handful of potential choices now
Take a look at the Kenwood DMX-110 BT for instance !