I have a 1 year old ruger 450 bm (no iron sight's) matched with a Leupold VX Freedom
3-9x40. On a bench this thing is a tack driver, farthest shot was 175 yds... however non bench hunting... I struggle.

I have always seemed to shoot better with over/under scope mount's.

If I were to pull the scope off and change the front mount..to something that sit's higher.... then the rear.... then re-mount to rifle...

How much would 100 yd zero be off? Say I rose the scope 1/2 in...

Would I need to redo everything?

I couldn't imagine anything good coming from raising the front mount.  You should try adding some sort of cheek rest to the comb of the stock as that will likely help substantially.

Anytime you swap mounts you should expect to rezero.

1- What is an over/under scope mount?

2- Is the current scope mounted with two separate rings? If so, are you asking about changing the “front” one to a different height than the rear?? (I am confused)

3- If you remove the scope and change how it is mounted, you will have to re-zero it.