I began two very minor changes (petcock and longer rear shocks) to my new S40 today and came up with a question regarding shock fit.  I did search the forum for some info prior to (and during) the install, as I like to be as self-service as possible, but came up with some conflicting info... so sorry if this question seems redundant.  

I read that 12.5" shocks would fit without mods (or so I thought) and since I found a good deal on some 12.25" units, I went with those.
However, the right rear foot peg hit the stock pipe (which was also slated to be replaced) before the e-t-e length reached 12.25" so the pegs had to come off.  As it turned out, once the pegs were off, the swingarm itself then hit the exhaust (just barely) before the e-t-e got to 12.25" so now I'm pegless and exhaustless.

I knew from reading the forum, that the chainguards would have to be modded a bit, which I think I did adequately (see pic), but I'm wondering if there is anything else (mechanically) that I should be looking at as a result of the longer shocks in regard to fitment?  I'll probably mod the chainguards a bit more before it's all over, but I think I got the two spots that were problematic.            

Thanks!

B.  

p.s. Yellow arrows show where I removed a bit of material for clearance.  

I think you've found the interference's I dealt with.
It's worth it.  

This post describes my experience with rear shock installation.  You didn't mention what configuration you have (cruiser, standard, cafe, tracker, bobber, etc.).  IMO, anything over 11.5" shocks on a cruiser config will look pretty strange, and the steering will get too twitchy, and the belt will be very hard to adjust (too loose with shocks extended, too tight when partially compressed).  But that's just my opinion, and I am far from an expert on suspension as you will see if you read the post.  The post describes my struggle with the rear shocks and front forks.  I feel like I have improved the suspension, and the handling is better too.

http://suzukisavage.com/cgi-bin/YaBB.pl?num=1633394130

Let us know how you do with your project.  Good luck.