The only difference in the schematic for model B is that the trace from PB1 to LED connects to PB0 instead of PB1 - otherwise it is exactly the same. The schematic online for rev3 is the same as the schematic for Model A, so there has been only one LED change, and that was for the I2C reasons given.
The LED (whether it is on PB0 or PB1) make the pin impractical for using the internal pull-ups - in fact on an attiny I generally don\'t use the internal pullups becase they have a very high resistance (over 25k) and are a bit picky. Hence the pullups on all of our I2C boards. (I\'ll add a note about this to the wiki when I have a moment)
If you cut the trace it will work - any reason you don\'t just pull it high (instead of pulling it low), that would work - or you could use a different pin.
R5 depends on what LED is - in the case of Model B boards it is 680ohm and LED is 5ma Green 0603. As is often the case, some value get determined for each run of the board based on the available parts, that is why they aren\'t on the schematic. Just about any LED (and corresponding resistor) would be a challenge for the attiny\'s pullups though, so this will be a common issue with most boards smaller and cheaper than the ATMega series.
Hope that helps,
Erik