I will try to be brief this time:
1) customizing your guitars is not wrong, they are tools, make them work the way you want unless you are worried about resale (and then just keep the original parts)
2) P90s are un-stratty, like a toothier humbucker with single coil openness... great pickups though, I used to swear by them much to the annoyance of sound and lighting guys allover the USA. Hum city!
3) I think the tremonti is just the wrong PRS for you, its mostly LP and LP jr DNA, you are looking for a PRS with some actual fender style singles with pole piece magnets (this is the difference between a fender single and a soapbar, P90 style pickups have bar magnets under the coil whereas 90% of fender pickups use magnets as the poles and vintage correct ones don't even use a bobbin, the wire is wound directly on the poles) maybe a bolt-on, possibly a trem and DEFINITELY fender type woods... I don't know all of his models, but if you ike the feel of the PRS you have already you might want to just find another model that has a stratty sound.... so, you know, stay away from signature models next time...
4) if you buy a neck to put on a strat you will probably want a '59 Gibson type profile and 50s Gibson nut width on a 25" scale.... the current Mexican 'classic' series is an excellent value on the used market and great for modifications... I am not sure what's poking you when you palm mute on a stock strat, maybe the strats are set up wrong or you are muting too hard because the little saddle screws shouldn't dig into your hand.... I have only had issues with cheaply made and badly set-up strats, with my own Stratocasters I've been able mute and chug away all night without issue
5) have you considered getting a gutted Gibson SG special with the late-period batwing pickguard and then building a new pickguard up with strat pickups and switching?Gibson actually made an SG with 3 strat-size blades too
http://archive.gibson.com/Files/USA/2007/SG3BFICH1_.jpg
but if you go SG special it'll be cheap, you can get the strattiest electronics possible, and you are guaranteed a wide and chunky neck feel. Only downsides of the 3 pickup SG is the scale and that all mahogany guitar are on the dark side, but if its way too dark plugged in you can always raise the potentiometer values to let more treble through. It won't make it a strat but will get closer.
okay, that wasn't brief