You need to be careful when driving in a pilot bearing that the driving socket only contacts the outside of the bearing. If it presses on the inside, it will ruin the bearing. Sounds like that may have happened. To get it out, stuff grease in the hole, then take a dowel or metal rod about the same size as the inside diameter (ID) of the bearing. When you have enough grease in there, put the rod in the ID and tap it with a hammer. The grease will push the bearing out. You may have to add more grease if the rod bottoms out.

As far as flywheel bolt torque goes, look back a few posts on this thread. I posted a copy of the FSM page that tells you all the specs on that. I believe it's 30-40 nM and then an additional 90 degrees. AKA very, very tight. New bolts should be used if the waists are smaller than specified.

-Dan

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1976 w115 300D 4-speed conversion!!
1985 w123 300TD 4-speed conversion!!

Non-Mercedes old stuff:
1941 Buick Special (Straight 8!)
1946 Luscombe 8a
1947 Willys CJ2a
1950 Chevrolet 4400 dump truck
1954 Chevrolet 3600 3/4 ton
1954 Cessna 195B
1955 John Deere model 40
1991 Ford Taurus SHO
2013 Jetta SportWagen TDI 6-speed (I sold out...