What MORSNO said!
Tighten everything up.
Check the steering post plastic bushings, the tie rod ends, ball joints (top and bottom), inside/under the motor drag link ends...Also the bushings in the skis to the spindles.
Replace the fuel and oil filters.
Clean the injectors (I use witchhunter)
Pull the fuel tank and completely remove the pump and pickup assembly.. carefully inspect the lines/hoses for ANY wear or cracks... the ethanol in the gas these days is wreaking havoc with the hoses.
Carbides on the skis... replace if necessary.
Set your toe in and camber according to factory specs.
When you do the pistons... pull the engine... clean everything up well... inspect the throttle body boots and airbox. Check the bores carefully, get them re-plated if needed. I'm a fan of a quick hone.. but most shops don't have the diamond hone needed for this and/or get carried away and wear thru the plating.
Have the clutch balanced and gone through.. I've used Indy Specialties and have had great luck with Dan's work.
Replace the Jackshaft bearing. Check and replace if questionable the driveshaft bearings. Check the motor mounts. Check, very carefully, the throttle and oil-pump cables at both ends for fraying or wear... replace if any sign.
Rear suspension... Pull it out of the sled completely... disassemble and clean ALL the old grease out and check for worn parts...reassemble with new Redline CV-2 grease. (DO NOT use trailer bearing grease or other generic grease).
For the money.. invest in a good basic shock package, front and rear. Zero Pro shocks are a good bet... I'm also a big fan of the Walker Evans dual-rate-sprung clicker shocks front and rear on a budget.
A good front bumper is a great investment.
Then on to running boards with your budget and the shocks on the list.. I'd go for a set of powder-coated Better boards. Easy to install and work very well.