What are the effects of a player playing out of his "natural" position? For example, a right-fielder playing center?

There is a formula to this, which was developed thanks to some insightful input from none other than Knuckleball Lover, a CSFBL beta tester! (Who knows if he remembers...)

Positions are "ranked" in order of difficulty:

 SS-2B-CF-3B-LF/RF-1B

When a player plays out of his natural position, his Range and Glove ratings are adjusted depending on how many "jumps" to the right or left.

 1 step left:  -10%
 2 steps left: -19%
 3 steps left: -27%
 4 steps left: -34%
 5 steps left: -40% (maximum)

Moving to the right is a little different.

 1 step right:  -8%
 2 steps right: -6%
 3 steps right: -4%
 4 steps right: -2%
 5 steps right: 0% (maximum)

What about catchers?

Any player moving to catcher loses 34% of his Range and Glove. Catchers moving to other positions are considered one step to the right of 1B. So, a C moving to 3B (three steps left) would lose 27% of his defensive skills.

A player trying to become a catcher requires 80 games a season at catcher + 400 total games at catcher for the career in order to permanently change.

The changes are applied to a player's actual ratings after fatigue is factored in.

What about changing positions?

A player's natural position will change if he plays 80 or more games in a position that is not his natural position. The actual position change will occur during the next season rollover.

At this point, a player's actual ratings will permanently change as if he was playing out of position (not a penalty because it's the same effect in the game anyway). A player's potential ratings will change also - if moving to a harder position, they change by the same percentage; if moving to an easier position, they will increase, depending on how much easier the new position is. As a result, a player moving to an easier position has the possibility to become a better player at that position over time.

The effect of multiple permanent position changes over the course of a career can hurt a player's overall fielding skill. (Players do better when they get to specialize.) The extent of the ratings changes is based on the extend of the position changes. A shortstop who flip-flops with second base will have a negligible drop; but a first baseman who flip-flops with shortstop will see a significant drop if he continues these bad habits!