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...the error is in the positional adjustment and the "static replacement level adjustment"...
I think the problem is that we use other marginal players at each position to represent that position.  But the players selected from the minor leagues to play short are selected for specific skills that are often different than the skills selected for in full time starting options.  When you lose your starting shortstop, 9 times out of 10, the guy replacing him is chosen because he is seen as reliable on DEFENSE exclusively.  Further complicating matters is the fact that the 4th outfielder is chosen with different criteria than the 5th infielder for different reasons.  The way we've gone about defining positional replacement levels is inherently flawed because it's inherently empirical and has no logical basis.
I also think the way to find a player's replacmeent level is not to make some linear adjustment based on playing time but to directly calculate what a replacement level player would produce in a given amount of playing time using pythagorean logic.