Mo,
Really hesitate to join in on this, since I'm not entirely convinced that your obsessive nature in tinkering with your guns is not doing more harm than good, but:
You remove the springs on the Mauser just like you do on the Mosin.
On the Yugo, you'll find two holes in the wood on the OPPOSITE side of the stock from where the springs engage their bands.
With an appropriately-sized pin punch, you insert that punch into the forward hole, and tap it carefully into the hole (avoid angling the punch or enlarging the hole) while driving the spring out the other side.
One thought in altering that spring- On mine, there's a notable gap between the spring shoulder & the band, almost 1/16 inch.
It requires no contact, on the FRONT spring, with the FRONT barrel band, at that SHOULDER.
The "button" on the spring & its hole in the band are obviously what retains the band in place.
You need full engagement with the button inside that hole.
If there's contact with the spring shoulder & the band that's preventing moving the band far enough back for fully centering the button in the hole, removing material from the spring shoulder to eliminate contact till you CAN center the button MAY fix the problem.
I don't know what you did the first time you disassembled the gun that left it in such a state that things didn't line up afterward, but this MAY help.
Something else to consider, IF the button does line up & pop back into its hole, is that you may have seated the spring deep enough to leave the button riding too LOW in its hole for positive engagement & retention.
You might, before punching the spring out entirely, just try to nudge its shaft slightly (again, with the pin punch on the OPPOSITE side of the stock) in the stock to leave the exposed spring riding fractionally higher.
I've done this with a Mosin that had wandering barrel bands, and as long as you don't screw up the shaft hole or do it repeatedly, the spring shaft typically stays put in its new "depth".
See if the button rides noticeably higher in its hole.
If that makes no noticeable difference, and/or the shoulder on the spring is contacting the band & preventing the button from lining up, you might remove the spring & just file off enough of that shoulder to let the button & hole line up right.
CAUTIONS: The less you fiddle, the better. I would not have messed with the sanding you did, at all. You MAY have changed tolerances somewhere in the wrong direction when you did that.
When you do things like that, you may think it's pretty simple stuff, but when you don't know what you're doing you can easily miss the fact that altering what's right in front of your eyeballs may shift something somewhere else in a spot or relationship that you don't see.
The general principle of gunsmithing is to make alterations to the smallest (as in "cheapest to replace") part.
I would not be whittling on the stock until other methods have failed.
I would not try to bend the spring, except possibly as a LAST resort.
Disclaimer: Not knowing what else you may have done to that thing, and not being there to analyze in person, any suggestions I've made here are to be considered carefully & thoroughly understood before you go ahead with them.
YOU are responsible for any further damage to the rifle, not me.
Denis