Welp!,... jetted right, a filter n' muffler is good for 2 to 4 horsies...
One muffler won't make much difference over another, due to the pipe diameter, exhaust manifold torque hump, and the valve size... but any aftermarket muffler will free up a little breathing over the stock one.  Same for the filter,... it can't breath in any harder than it can breath out...
...but it's a 10% increase... Good enough for a real "seat of the pants" difference...

... and my best advice for jetting is,... more is not better, unless it is better...
In other words,... don't just go for the bigger jet because you think it will mean more power,... you can end up with a loud, smoky, burping, farting, pig...
Bigger jets don't make more power... the correct jets do...
In Mikuni jets,.. I'd guess you are in 150 to 152.5 / 50 to 52.5 range... with 1/2 to 2/3 spacer... (totally guessing ) (don't know dynojets)...
Make changes, evaluate the results, and make your next move based on those...

... and have fun testing it out, and learning...  ...



PS... sorry about the "unexpert" advice,... I only answered 'cause nobody else did...BUMP!
I don't know why people go the "dynojet" route at all.  Some reason I don't know, and probably should. Maybe some other dynojetters will have more specific advice, or can straighten my a$$ out over why we should all have dynojets....
... no offense...

I installed my dynojet kit a couple of days ago and it was pretty easy as long as you don't have to use Te drill and screw. I had to take the whole tank plus The battery Holder. I just don't have enough tools to play around. The kit tells you to use the DJ 144 but apparently that is too lean for the bike. Read this post about my bike. I have a K&n air
Filter, and a Dyna muffler plus the jet kit.

http://suzukisavage.com/cgi-bin/YaBB.pl?num=1299001370

The stock jet for the ls650 is a 145 and according to this chart that dj144 is less than the stock jet.

If I was you I just return the kit and talk to lancer
To get you a really good set up that matches your bike.

He's out for a couple of weeks but leave him a pm and he will get back with you soon.  what is the largest jet that your kit has?? The biggest one i have is the DJ146 i might just go ahead and install that one till i get the chance to get a performance carb from lancer.