Hello all.. I am a new 2006 S40 owner. I bought the bike a little over a month ago with 3300 miles on it and now have nearly 4000. I was a little unhappy with the backfiring and poor top end performance so I have installed a Stage III jet kit (yes, I took that on myself), a Jardine slip-on and an NGK Iridium plug. Backfiring is nearly completely eliminated after these mods and tinkering with F/A mixture and my top-end is up from 81 MPH to 92 MPH. I've also had to replace the front brake pads, as they were squealing, and re-seat my upper riser bolts with some loctite, as they seemed to be vibrating loose. In the past 100 miles, my rear brakes have begun chattering at low RPM and appear to be adjusted properly. Are we talking rear wheel removal to change out the shoes? That doesn't sound like fun, at all.  
I'm also unhappy with the "stock" saddlebag fit but understand there is a clearance issue due to the design. Have the rest of you with saddlebags secured the bottom of the bags to the guards with some kind of aftermarket bungee/tie downs?
I'm looking to do the 4000 mile service myself, including a valve adjust and oil change. I read through the oil recommendations thread but really didn't find anything completely conclusive. Synth or Standard? Recommended brands?

Thanks for the awesome forum and I hope to be a valued member!

Glad everything worked out for ya!  You might have had more response to your question if you'd posted in the "Rubber Side Down" thread, that's where Savage questions usually go.  This thread is more for established procedures.

On a side note, I've got the stock bags, and my biggest problem was having to patch the straps when they started to crack where they go through the buckle.  I have a zip-tye going through the rear of the two loops on each side, and loosely fastened around the bag support.  More to keep them from possibly flapping around when empty, than anything else.

The front brake pads need replacement only they're worn thin, 1 mm or so.  Squealing is coming from the steel backing plate, and auto parts stores have several products to lube the back or to coat the back to damp the squeal.

I'd use no less than any 15W-40 diesel engine oil.  Any top brand will be very good---Conoco/Phillips/76/Kendall is my favorite.  Or a syn 5W-40 diesel engine oil if you prefer.  Or a 20W-50 motorcycle engine oil, especially in your summer heat, or a syn xW-50 motorcycle engine oil...just about any oil except a 10W-40.  The main advantage of a synthetic is that they're thinner when cold, not a concern in your area, and thin less when very hot, good in your area.  Also, they oxidize more slowly for longer oil life under very hot conditions.  HiProFiltro has a good $5 oil filter and $15 air filter.  No need to pay more.  You'll get these at a non-Suzuki shop.

http://www.hiflofiltro.com/17.0.html?&L=0&sel_uid=1290
HF137 oil filter
HFA 3608 air filter

Note that this outfit makes the motorcycle oil filters for K&N.