Rolf, the bottom holes below the flippers should have nickel-plated wire that sits on the playfield. Designed as an anti-cheat so the ball does not easily bounce back into play from below the flippers. As for the holes in the middle, yes, I would fill and color match. Duct tape is a creative idea for the area up top that gets hammered from the constant kick out hole wear. I would touch up as best as possible then clear all to protect. There are several good resources on the web for this type work. Cliffy did one a few years ago with Varathane clear (I also use) that demonstrates what can go wrong (color shift, chemical reaction) here's the link to his efforts: http://www.passionforpinball.com/jjresto.htm

Lastly, Melamine foam (Magic Eraser) and 91% alcohol will do the best job of getting the deep down dirt out.

I would check with PBR first, if you have other parts you need. If he doesn't have a set, many on this forum will have spares from games they have parted. The spacing looks to be standard about 3" long.