While the Jap action is considered quite strong... a small backing out of a primer is not a great concern to me... how "flattened was the primer??? but... anyway
You can measure, CRUDELY, headspace without guages. You take a new case, unfired. You may have to dis assemble one of your rounds... Unfired 6./5 Jap brass is a little scarce last I looked. And "shim stock." You can get it at larger hardware stores or cut up a "blade" style feeler guage which has an assortment of thicknesses--hit the 2nd hand stores.... You affix a piece of shim stock to the base of the case with light grease/oil, and try to close the bolt. Best to remove the extractor so you get maximum feel and work GENTLY! As I recall, minimum should be in the .004 range. Normal runs .004 to .007. .008 is on the edge. And as you exceed .010 you are into DANGER ...
The added help here, the 6.5 Jap is semi rimmed. If you are stopping (headspacing) on the rim --I don't recall what spec is for this round... .38 Super stops on the tiny rim, that is a little easier to see. I know the .220 Swift is semi rimmed and headspaces on the shoulder... If you are headspacing on the shoulder like the Mauser family, you have to be very very gentle and then the reading is not the very best, but will give you an idea if you are into "field guage"/danger territory.
The gunsmiths with whom I have worked have uniformly told me that the "go" guage is a manufacturer's tool. It is for seating the unfired barrel in the action. And it needs to be just loose enough to not close on the "no-go" guage. Many, many guns after they have been fired a number of times, will eat a "no-go" guage without trouble. In the military use, the "field" guage was so long that the gun was completely unsafe and probably the firing pin would not reach the primer...but the case would come apart if it did... Very poor tool to issue a soldier.
Oh yes, if you ever section a case... saw it in two, or grind half off on a grinder... you will see the brass thickens alot in that area just ahead of the extractor groove. This is why the brass does not expand like the shoulder. It is the pulling apart just ahead of this that can release hot gases at twice the temperature of a cutting torch and if the right parts of the gun get "cut" you are dead if you are lucky or getting your face rebuilt if not and wearing dark glasses... best of luck.