Alright, I'v been looking around on the site for a while and have seen a plethora of mods for this bike and they all seem to have their own specific missions to remedy a particular issue, however I have been a little lost in some much content lol and I had a request for some of you bike guru's out there.

If you where to put in order of importance a list of your recommended modifications so I can get an idea of what I should be prioritizing that would be awesome. I am starting a new job so unfortunately I don't have all the money in the world right now which is one of the main reasons I wanted to do the most important things first.
I generally prioritize reliability, safety, fuel economy, comfort, performance, and last appearance.
I appreciate any suggestions you all might have and I look forward to hearing your thoughts.

If the bike runs well and does not have any flat spots in the acceleration, don't worry about the jetting.

Stock vacuum petcock....get rid of that ASAP and use a genuine Yamaha Raptor petcock....not some Chinese $ 6 copy.

Air cleaner...the stock paper one works very well, and lasts a long time if you don't ride on dirt roads.  When folks suggest a K&N drop in - it is the replacement for the stock filter - not a cone filter.

The Cam Chain Tensioner needs to be checked as you approach 12,000 miles....sooner if you ride a lot of short trips.

The DYNA muffler is a nice upgrade - if you find the stock muffler just a bit to tame for you.

Ride the darn thing for a year and see what bothers you about the bike.  Saddlebags or some form of storage is nice if you want to carry anything.  A windshield work for some - I have a full face helmet and like to ride without a windshield.....however I have a bike with a windshield and ride that when it is cold or rainy.  My Savage is a fair weather bike if I can plan it.

 

Before I have an opinion I'd wanna know year and miles..

I think Dave nailed it well......

Personally speaking of my own experience ( mostly short every day commutes in pacific northwest ).

Rotella

Versy

Metzler or equivalent tires

Wind screen  

Depending on what your goal is:

Safety(first):
- Replace the IRC stock tires with not-IRC(tm) tires. The tires that are not-IRC(tm) tires are darn good tires  
- 90 degree valve stem on the rear wheel to make tire pressure checks easier.

For longevity:
- Verslavy CCT
- Raptor Petcock.
- replace "phillips" screws with stainless hex fasteners (carb, side covers)
- Consider getting rid of the chrome head covers. They serve no purpose.
- Pull the brass plug covering the idle mixture screw. It infringes on your right to adjust your idle mixture.

Comfort:
- Raise the seat height 1 inch.
- Forward controls.
- Install one of the recommended fixes to mark your last fill up. (bike computer, grease pen, luggage lock, knit counter).


There is no "Economy" category, you won that battle when you bought the machine. Now it's all about making it to the "Mileage Hall of Fame".

I sure liked the drag bars that came on my 2005..

The K&N Drop in goes into the stock air box, and fits just like the original paper filter.  This really isn't a performance upgrade on a stock bike....the paper air filter flows well enough for the needs of the stock carb, cam and muffler.  Over the long run the K&N drop in can save you money as it can be washed, oiled and returned to service.....whereas a paper filter eventually becomes clogged (but that takes a long time if you ride on paved roads).  You might as well just use the paper filter until it is ready to be replaced.

A cone filter clamps on the end of the carb throat and eliminates the stock filter system.  It is more of a "fashion" statement than a performance mod on a stock engine  - as the filter can be seen on the back of the carb, and can be soaked with water when you wash the bike or get caught riding in the rain.

The best way to figure out if you like bars....is sit on someone else's bike and try their bars.  My 2004 had the stock Suzuki Drag bars and risers, and I think they were more comfortable than the buckhorn bars...which seem to require you to angle your wrist in a weird way.

How tall are you?  The forward controls help to adapt the bike to taller riders.  I am 5'-8" and was comfortable with the stock peg location.  And yes, you can make your own if you have fabricating skills......