Hi Bluedeath,
Love this mods.

Some comments:
1. Getting rid of the PCB and replace with standalone hats and buttons
The best place to get stand alone HAT - with different covers:
http://www.splash-one-bandit.com/parts.htmlAnother, probable made by CH - not really cheap:
http://search.digikey.com/scripts/DkSearch/dksus.dll?Cat=1114837&k=HATSFS modifications: (needed for repair damaged part and to keep button count low in order to use it with the FLCS)
If you dont play really old games consider put a independent USB controller inside SFS - cheap DIY Mjoy8/16 is good option.
4. lower part of the base box completely redone (same kind box as the joystick base).
With independent USB controller inside SFS you can consider make one base Warthog lookalike, due more buttons and axis available.

F16 FLCS modifications:
1. accurate pinkie switch
Ask Splash One Bandit for this, they make a very good one.
http://SimHQ.com/forum/ubbthreads.php/ubb/showflat/Number/3123525/Searchpage/1/Main/320489/Words/splash+one+bandit/Search/true/Cougar_Paddle_Lever.html#Post3123525
TQS modifications
1. “eraser head” replaced with hat switch or mini joystick
Any is fine, for some games HAT (buttons is more useful) for another's mini-stick (axis).
Mini-stick source:
http://yhst-27389313707334.stores.yahoo.net/thumbjoystick.html
3. If “eraser head” won’t be replaced by joystick available pot connections will be used for trimmers.
Original "Eraserhead" dont use axis (pots) just buttons.
1. I understood quite well (I hope) how the BIC pen magnet arrangement works for TQS but I have some doubt on what to do on the FLCS, if I understood correctly the A1302 can read the angle of the magnetic field between 0 an 90 degrees
For practical use you are limited to around 40 degrees. So "BIC" assembly is fine to FLCS too.
Since the pot has a throw of 60 degrees should I mount he magnet in some sort of “fake potentiometer” configuration o r directly on the Joystick gimbals axis?
In original F16FLS pots pots rotate only 35~40 degrees. So put magnet in joystick gimbal axis (or in BIC assembly) is more easy.
2. Can the Doc flier’s mod be applied to the SFS also (I would like to avoid to build a transmission shaft if possible)
Problem with SFS is that your levers travel too much, around 90 degrees, and the original pot have a huge linear travel. I think that DIY HALL assembly (like Doc Fliers) in original pot case exced the usable reading angle (~40 degrees) of these HALL sensor.
Read that Mike Powel (mikesflightdeck.com) say about useful reading angle of HALL sensor here:
http://www.mikesflightdeck.com/old_stuff4.htmGood luck whit these (big) project, and keep the news coming.
Sokol1