When I'm restoring a pin, I always remove the old factory mylar, and replace with new mylar in the same areas as factory. Sure you will not be abusing the pf as much as a sited pin was and you will be cleaning and waxing more often, but the factory did put it there for a reason
Hole protectors are up to personal taste. If I was using then I would use the ones that don't protude onto the top of the playfield, they look better for a new pf,
Like this http://www.mantisamusements.com/taf.htm
 if you have to cover existing wear then cliffys would be the way to go.