I have a 05 S40 that have never ridden, bought from used car lot at Christmas for $3000  only has 6500 kms on it. windshield, bags. fork bag,highway pegs   and new passenger back rest and rack in box  and frt driving lights and bar in a box.  started it few times on warm days this spring. went to ride it last week and it made a hell if a clunking when turning over  took off seat, tank  and left side chrome on the head.  the noise is coming from the decompressor, unplugged it, no more noise. but now.no more compression,  is it possible the  valve hit the piston ?

I noticed the clunking before the starter starts  when i tried my 99 savage it suprized me but its the decompression valve and its normal,  hook up the decompression valve again and don't worry about it unless the Clunking continues after the bike starts up. i had an old suzuki atv with a manual decompression valve and with the atv running if i hauled up on the valve it made the clunking noise so if its doing it with the motor running then the valve could be sticking. there is a round actuator that activates the decompression valve under the tank that might be corroded possibly or it may just need to be adjusted there is info on here about adjusting them etc..

Justin,  it ran fine when first bought it .ride it on my trailer just before Christmas at 30 below.  put it away in the shed till warmed up, started it few times in the shed ran beautiful.   then tryed to start it few weeks ago and the clunking began, has never run since, beem trying to rebuld my garage that burnt down Nov 8.13..  no time to take the head off the bike.
heres picture of the day I bought it. was 30 below 0...  brrrrrr  

I ordered a shop manual for it.  when get it and my shop finished,,will tackle it.   here the old shop Nov 8 ,fire. here the new one 1/2 done.