From the previous design there were some takeaways of what to aim for;
 1) Continue with the two piece design 
 2) find a reasonable size SMD header
 3) find energy storage that fit

Knowing this I went back to where a lot of time is spent, digikey's parametric search. As I was browsing the super capacitor category by lowest height with a minimum of 1F capacitance I came across some very interestingly small but with large storage HVC caps. On further investigation it turned out this was because they were hybrid caps! this means they weren't true EDLC supercaps. That being said those their rated was 15F! and a single cell was only  12x12x2.5 tall! I thought to myself surely there must be a catch but I can't not play around with these. 

So with sails unfurled I start designing my next amulet. I tried to find the lowest profile SMD that would be easy to solder and settled on a 6 pin 2.54mm header. Also while working on this version I decided to experiment with overall height I tested out using 0.8mm for both base board and face plate pcb thickness.

For charging I had to dig into the data sheets and supplemental material. Luckily Vishay had some pretty solid documentation. These type of hybrid caps need a lot more care when it comes to charging. Up until now I've been drawing power straight from USB, depending on temperature these hybrid caps I chose have a max voltage of ~2.8.They state that ideally constant current/constant voltage charging scheme would be used. However a current limited LDO could suffice. I'll come back to charging later, but for simplicity and cost I went the LDO route. There were some draw backs to this, i.e. no way to protect from overcharge and no integrated charge indication (stuff you'd find normally in a battery charger IC). But for now it would suffice.

The result:

Some explanation on the pictures. The only surviving one of these I still have! The goopy look was from me experimenting with conformal coating. You can see I even spelled hyat wrong! (حياة) ! I was just getting into learning arabic at the time (still have a long ways to go!). Not pictured are the standoffs which were standard threaded hexagonal standoffs, and the hybrid cap which was harvested and reused on other boards.

Ok, so the 0.8mm looked awkward with the amount of space between board, and wow we have so much space? Maybe too much space. Was happy that the design worked, but unsatisfied with the height.

Improvements over second attempt:
* surface mount headers replace standoff power and hence safety from shorts
* much more dense and low profile energy storage