Dude, I felt exactly the same way. And the funny part is that modifying the body was probably the easiest part of the entire project. Two quick knocks with a hammer and flathead screwdriver was all it took to remove that extra torso section, and another two knocks to pry open the upper chest to glue it all back together again.
The toughest part for me has definitely been the outfit. Melting the gloves off the mail hauberk was a bit of a hassle, but nothing compared to getting his darn belt back on. One of the shoulder straps that attaches to the back of the belt was WAY off-center, so I ended up cutting the threads holding it in place and gluing it in a better position. But when I tried to put the thing back on the figure, the glue gave out. Another repair, and this time the small leather strap that secures the belt around his waist came undone, so more gluing was required for that repair.
It seems to be holding for now, but I guarantee I won't be doing any more tweaks on that belt anytime soon. I'd have sewn the thing to make the repairs more permanent, but I think you need a special kind of sewing needle to make stitches that small.
So, don't fret about the body modification. Even if you make a mistake it'll be covered by his outfit. But make sure you take your time when dressing the figure afterwards. Don't permanently attach his boots or gauntlets until the very end to make things easier for yourself.