The head was the major difference factor. These motors needed more compression and loved it!
I rode a XRS in '07 with a few simple mods, and sold everything under the sun.
-I re-cut my head locally to my specs. Cheapest way if there's a trustworthy shop in your area. Otherwise spend the money on SLP or a Terra Alps head. Added bonus for a aftermarket head is extra cooling capacity. It's easy enough to raise compression, THE REAL REASON I buy a a/m head is for the extra cooling they offer.
Also I found much more airflow going through the machine without the heat shielding for the motor wrapped in there.
-The pipe made a very small difference. I'd keep the stocker and remove the heat shielding. Only if you get it ceramic coated though. I think this rivals what many pipe manufacturers offer.
-The can is totally on you, we live in MBRP country out here, HPS seems to be the choice for many though.(I have mixed feelings, I think its dependant on the sled and not brand of silencer)
-I sold and set-up a few SLP equipped sleds(and ride an '06 because of the performance delivered on my powertek) and they give you the edge on your buddies. Pull you about even with the stock machines of today. But same applies if doing the same mods without buying a "kit". You end up on a similar level of performance if done in conjunction to setting up the overall package.(transmission and suspension)
The bigger influence on your decision should be the clutches, gearing, and suspension set-up.
My "stock" XRS with head work, clutching and gearing fought tooth and nail with said machines everyday we went riding. My customers are savvy and tune their own sleds to a point, some I do all the work to, however giving them as much insight as I can without overloading them.
One friend in particular had his mind set that the Lite track was garbage(I would never recommend a Lite unless living in Padagonia where the snow is rock hard) so we installed a 2.5 CE on his sled and I kept the Lite.(determined to make it work.) My friend never touched his suspension, I helped with the clutching and gearing, and he had the full "pipe-head-reeds" thing going on. But he never touched his suspension.
With the help of the forum and Turbo Al amongst others, along with my own ideas, I found a combination that worked extremely well for our snow conditions that made my "stocker" perform on the same scale as the "modded" machines. While they made 10 more hp(?) and had better tracks, the overall package was no better than my mostly stock machine. I spent under a grand for what they achieved for 2-3k range. Simply putting together a overall package of engine-suspension-transmission is easy now that so many of us have the experience and have ironed out the details on machines 3-4 years old.
*Disclaimer - Not to say the SLP set-up is wrong or bad in anyway, because my '06 rocked with the SLP clutching and gearing, I just took it a level I wanted which had different characteristics than what the SLP set-up offered.