If you retain the stock throttle body, the Harley Heavy Breather for Touring Models will not fit. The hole pattern for the three attaching screws (air cleaner to throttle body) was changed for the '08 model.
As for the fairing lowers, Harley did come out with a shorter element in 2010 to make the HB work on bikes with lowers. Still doesn't work with the '06 throttle body however.
28716-10 Compact Design – Chrome. $299.95
Fits ’08-later Touring models equipped with Fairing Lower
Glove Boxes. Slightly shorter cone-shaped element provides
clearance from the fairing lower. Street legal when used with
Original Equipment throttle body.
I believe you can still do this however if you want to buy the version they have for the Dyna and Softail that will also fit the '06 throttle body on Touring models. You might have to buy the shorter element separately if you have a clearance issue with the lowers.
29098-09 Gloss Black. $299.95
29299-08 Chrome. $299.95
Fits ’08-later Dyna® and Softail® models. Street legal when
used with Original Equipment throttle body. Also fits ’99-’07
Dyna, ’00-’07 Softail and ’99-’07 Touring models (except
’99-’01 EFI Touring), and models equipped with 50mm
Throttle Body P/N 27623-05 (race application only). Does
not fit models equipped with fairing lower glove boxes.
Jerry