Steve,
I'm currently running 17's and AVO lowering springs so no problems there ! I don't know if the Offset and PCD of the 7th Gen is the same as the 5th gen you've got. IF the tyres are the right size then the speedo will not be out, if you increase the wheel size you reduce the tyre side wall. (I run 215/45 17's).
On the alignment note, I reckon it's always worth having it done (potholes can knock it out) especially when lowering the car as the geometry get changed. Mine felt like a different car last time I had it done (but it was way way out ;o) )
On the transmission noise note, what sort of noise is it ???? The engine will rev slightly before the "Clutch" part engages at around 30 and out of sports mode (PWR) is it dropping down a gear when you accelerate ??? Try Putting it in 2nd pressing the "Manu" button and drive around on and off the throttle if it;s knocking it "Could be" a worn engine mount or a broken exhaust mount.
Pull the ECU fuse before fitting the HKS Filter leaving it off for about 10 minutes then go for a blast !
Best of LUck
HTH
Chipster [ICOC]
ST183 4-WS (Auto) 1991