I think your description of pin vs port and ddr needs to be fleshed out a little more wkrug, it can cause massive headaches for people that don't understand it.
The PINB register is directly fed from the port driver, it will always show you the actual voltage state of an I/O line, of it's 0 the line is low, if it's 1 it's high, the exact voltage where this transition occurs is listed in the PDF for your particular AVR chip. One neat trick on all but the oldest AVR lines is that writing a logic 1 to the PINB register will cause the corresponding PORTB bit to invert using a single instruction. (Ordinarily you would have to read the portb logically invert the value and then write it back) it allows extremely fast bit twiddling.
DDRB is the direction register, if a bit here is set to 1 then the corresponding I/O line is driven as an output. If it's 0 it's driven as an input.
PORTB is the register that determines the desired port state of the I/O line, when DDRB is 1 the I/O line is set to output, when the PORTB bits are set to 1 that I/O line will try source current, when it's set to 0 it will try to sink current. When DDRB bits are set to 0 (input) the corresponding portB pins will turn on or off the internal pullups on that I/O line. This is very important to know because if you're using an I/O line as an output that's set to high and then decide to switch it to input you may have problems if you don't account for the fact that portB was still set to 1 so the pullups are enabled on that I/O line.
Another thing to note about the pullup resistance is that there isn't infact a pullup resistor it's a cmos junction so it acts more like a current source, the resistance value given is an approximation of equivalent resistance.
One neat thing to note about all this information is that if you're using PORTB as an output you can use PINB to determine the ACTUAL state of the pin (not the logical state) this is a commonly used trick to measure capacitance via a fixed resistance, what you do is measure the number of cycles after you change the portB register until the corresponding PINB register actually changes state. If you have the time to discharge and know the resistance you can calculate the capacitance.