headers are a good start for supporting mods, and are much easier to put on at the same time your right. i'd also do a 180* T-stat, rockers or cam (one or the other), and CAI. those would be great supporting mods.

in this order:
180* t stat
CAI
Headers
rockers or cam

 

Definitely do the headers when you do the top swap if you can, because like you said, with the rear head off the car, they will be so much easier to install. They are also a great mod for a top swapped car. Don't get your hopes up on dropping pulley sizes though, especially with that gen 5 blower. With all the mods in my sig, I still knock at WOT with the stock pulley. I have a strong feeling my knock could be tuned out, but I'm not sure. I'd recomend that you have a way to scan for knock before you do the work.

 

dbl_d718, how much power are you putting down? also do you have a tuned pcm (zzp or other) or are you still on a stock 3.8 tune?

Okay, so definitely do the headers, and look into rockers. Already got the 180* T-stat.

 

I've never been on a dyno or at the track, so I have no clue what kind of power I make. I didn't buy a vendor's PCM, I've had PRJ do a custom tune for my car but we always run out of time before he gets it perfect. I'm planning on getting rockers and just leaving my car with him for a couple days and have him install the rockers and do a complete tune for me. If you can find someone near you that can do a custom tune, that'd be your best bet as it'd be way better than buying a PCM from a vendor.

 

Slap some 1.9 ratio rockers and L76 (L76- NOT LS6) valve springs in while your at it- these plus headers will allow you to run that 3.8 pulley knock free. I'm running 16.5* of WOT timing on mine right now with zero knock. You'll also make power for longer at higher RPMs and will be able to spin past 6000 in each gear.