You can take the PC out of the loop and re-connect all stock plugs in stock configuration. System will "re-learn" and go back to default F.I. settings.
A dealer can "Tweak" the stock F.I. map to get rid of the infamous 4K stumble if you've got it. Have them use the Yosh Box to do this, or if you can get hold of a Yosh box, you can do it yourself. I did mine. Takes five minutes.
Richens up lean areas, leans out rich areas. Better MPG, Better performance.
Aftermarket pipes are fine with stock F.I. tuning. I ran Remus Titanium pipes with stock F.I. settings. Then did Yosh Box tuning. Ran fine, better fuel economy, better performance everywhere. Remus were 18 lbs. lighter than stock. 70K miles. Perfect, no problems ever.
27K is a young bike. The Vstrom will easily go over 100,000 miles and many are there now. I had an early one ('02) and did have the clutch "Chudder", replaced it twice under warranty, and did a 3rd time using an SV1000 basket/bearing which eliminated the problem 100%. Your lucky, your '06 has the new design and is quiet. No other problems I know about.
On the road the Air filter is the only thing you've got to watch. In really dusty conditions can clog up quick. Some car filters work. Find out which.
Vstrom boards someone will know. Or go to ADV Beasts forum and ask.