Alright, so, I am at a fork in the road. I am trying to decide if I want to get a new muffler and put that on, or a smaller supercharger pulley and put that on. I just don't know what to do. What should I do first. I am leaning a little towards the exhaust and then getting the puller after. How much would it cost to have a Flowmaster 80 series installed at a shop without tips? I'm just looking for a rough estimate.

Get the Flowmaster from Jegs I believe for $80 + shipping, and take it around to different exhaust shops and get estimates. I'd think you should be able to get that muffler and have it installed, all for under $130.
Personally I prefer Magnaflow'*, but variety is the spice of life.
Also, you might find you'd benefit greatly from a www.justmagnaflow.com high flow catalytic convertor.
I'd wait for pulley because with the free'er flowin exhaust you'll have more gains from the pulley.

Like olblueeyes said, but the muffler from Jegs first. Then find a quality ma and pa place to get it installed. I paid $100 for installation of the muffler and tips that i had also bought.
Here'* the link for the muffler on Jegs:
http://www.jegs.com/cgi-bin/ncommerc...08&prmenbr=361

It'* the $79.99 one.

Magnaflow, bud. Magnaflow. It flows better and produces more hp.

After the intake and exhaust are done, slap in a 180° thermostat, and get the pulley.

I'm gonna go for flowmaster because I like the tone more, it has just about as good as performance flow-wise. I already have a 180 t-stat and the CAI, so the exhaust and pulley are on the "to-do" list. Hopefully by summer I will have both of them on, and then some.

Get the muffler ... then the mod bug is gonna bite ya!

I think it already did.

I'm interested in either the Magnaflow or the Flowmaster for my SE. What size is my stock pipe? 2.5"?

it couls be eithe 2.25 or 2.5 you should just go measure it, that would be easier than us trying to guess