Just updating thread with some new info I found:

Engine swaps: 996 3.4L

Engine parts:

--996 M96 throttle body and plenum off the 997 apparently fits too

Interior:

--Carrera gauge cluster - nice to be able to check the oil pressure and charge condition. http://986forum.com/forums/general-discussions/43017-carrera-gauge-swap.html

Exterior:

--2004 OEM rear bumper

--Front bumpers off the 996 and 996 GT3 fit onto the Boxster.

--Cayman spoiler (wing rather than an air dam) can be retro fitted

Steering:

Exhaust:
--2004 Boxster S muffler

Brakes:
--996 Carerra Front Brake Calipers and Rotors

--996 Carerra Rear Brake Calipers and Rotors

Suspension:
--RoW (rest of world) M030 european sport spec suspension

Wheels:
--Cayman S 18 Inch wheels -8x18 et 57 front with 14mm extended hub spacers -18x9 et 43 rear 5mm spacers (235/40/18 265/40/18)

--996 Carrera light Weight Wheels 18x7.5 front, 18x9 rear (225/40/18 front, 265/35/18 rear)

--Carrera Sport 19x8.5 et 55 front, 19x10 et 42 rear (235/35/19 front 275/30/19 rear) 11mm Brey-Krause Hub Centric-Extended wheel spacers front axle only. no spacers needed on rear axle.

--2015 Boxster Spyder 19 inch wheels. 19x8.5 et 50 front + 5mm spacer, 19x10 et 42 rear. (235/35/19 front 265/35/19 rear)

Tire sizes:

Drivetrain:
--987 shifter: 15% shorter through than the 9x6 shifter. The 2004 Anniversary edition Boxster has this shifter.
--997 Shifter: 997-424-010-00:
Just installed a new 997 shifter - Page 2 - 6SpeedOnline - Porsche Forum and Luxury Car Resource

Audi A4 FWD transmission swap:
http://986forum.com/forums/general-discussions/56662-audi-swap-2.html

http://986forum.com/forums/diy-project-guides/56663-audi-transmission-swap-diy-thread.html

Post # 2 in this thread:
http://986forum.com/forums/performance-technical-chat/57197-5-speed-transmission-interchange.html[/QUOTE]

Misc parts:
--Airbox: 987 air intake box: http://986forum.com/forums/447558-post14.html
http://986forum.com/forums/performance-technical-chat/32074-987-v-986-air-box.html
--987 air intake "Distribution T".

--Top - OEM top and frame from 2004 or 2003 into an earlier car. The advantages of a glass rear window over plastic are obvious. The OEM 4-bow top allows for a larger window and better access than the aftermarket retrofit tops. In my case it also provided a headliner that was not included with my 2000 base Boxster or earlier cars.

--Lights - OEM litronics (I also installed the self-leveling and low beam swivel feature.) While not technically from a later car (they were available starting in the 98 model year) they provide better illumination and are also an appearance upgrade. http://986forum.com/forums/general-discussions/54697-advice-used-litronics.html http://986forum.com/forums/general-discussions/55840-can-you-endure-one-more-litronic-thread-me.html

--OEM intermittent wipers. I don't think these were available on a base Boxster. I know some people don't drive their Boxsters in the rain, but this is nice to have on a misty day.

--Six-channel amp from a Carrera: http://986forum.com/forums/general-discussions/14815-6-channel-amp-pnp-speakers.html

--OEM seat heaters: Dennis Vogel: Projects - Boxster Heated Seats
I'm currently working on adding memory seats to the power seats I installed over the last few weeks. Here are some links: http://986forum.com/forums/diy-project-guides/59964-memory-seat-retrofit.html http://986forum.com/forums/general-discussions/58080-full-power-seat-installation.html

--Rear badging: The later chrome version of the 'Boxster S' rear badge, rather than the matte silver version seems to be quite nice, and also matches the exhaust tips if polished.

The Boxster S has the same brakes as a 996

Why would you want to put an Audi tranny in ?

Just a suggestion: As you update the thread, you can Edit it into the first post as well to keep the info easy to find at the front.