Welcome to the site !!
What you want to do is set the spring length to what it says in the manual (this is with the bike wheels/weight off the ground on a stand or crate , not the kickstand) , you loosen the top lock ring on the shock and then either by grabbing the spring from below by reaching in from the rear and grab the shock spring with both hands and try to turn it , or , if it won't move , then by using the punch you used to loosen the lock ring , to tap the bottom collar to turn it to get the desired number by either tightening or loosening the spring , probably a full turn or so depending on how far it is off , 1 full turn is about 1/2" of length ...... then measure the sag/distance from the center of the axle or a stable focus point that will not change , so when you make a measurement it is always from the exact 2 points that are as vertical as possible (axle to fender) , this is with the bike on the stand .... write that number down , if you are using a actual sag scale , you want that number to be 0 (zero) , then remove the bike from the stand/crate so both wheels are on the ground , then if you can , to be more accurate , have someone help you hold the bike level from the rear left side ....get on the bike wearing your riding gear , if you ride off road , and use a backpack , then wear it as well , basically boots , helmet and if used , a backpack , the pants/jersey/gloves are insignificant for measuring purposes , you can just wear your jeans/t-shirt ..... then sit on the bike in the natural sitting position , in other words when you stand on the bike and sit down , it is where you sit on the bike naturally (with both feet on the pegs which is why it is best to have someone help stabilize the bike) , when you are where you would normally sit , basically it should be in the low spot of the seat , then bounce on the bike a few times so settle the suspension ..... then sit there not moving ...
Now have your helper measure the sag number , write it down , what it should work out to is 4 inches/100mm from your original measurement ... you need to get this number established no matter what , now get off the bike , and measure the "free sag" , this is the bike standing on its own weight but without you on it , bounce the bike a few times by pushing down on the seat enough to make the bike squat , then release , do this a couple times .... now measure the sag again , this is the free sag ....
For spring length you should be between 9.6 and 10.2 inches in length
The free sag should be around 1/2" to 1 inch (about 30-40mm) , if it is not then you need a stiffer or softer spring depending on which direction it goes .... you can set your sag anywhere between 100-110mm , but you have to have the base settings first or it won't be right , so no matter what , you have to have 100mm as a set sag to start , then you will know if it is sprung for your weight or not ...
So to answer your questions , yes , you should readjust the spring to the standard setting and recheck the sag , you need this for a baseline , as all other measurements depend on this being set correct to the manufacturers specs , that will tell you if your good with the springs that are on it regardless if they are stock or not ..... so what you are trying to do , is set it to what the manual recommends , then get on the bike and measure , then get off and measure , if you don't fall within those limits with it at those settings , then you need a different rate spring ... , a little trick you can do if you are getting different readings each time , is to spray WD-40 on the shock shaft near where it goes into the shock body as well as the forks tubes right by the seal .... this will help eliminate any stiction ...
