Sorry, being an idiot in the realm of chokes (aside from chickens), could anyone give me some info as to what the choke is doing in the circuit?
Are there any variations to the specs of the choke such as resonance, resistance I can change slightly without causing harm the the rest of teh board?
Current specs for the choke are 100uH but there a lot of variations listed for resonance, amps, max resistance, etc.

Thanks

Choke? You mean the coil? The coil's purpose it to filter out noise on the analog pins. A more exact reasoning is given in the ATmega644 data sheet.

That said, Gen3 has no such coil and still works.

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Generation 7 Electronics	Teacup Firmware	RepRap DIY

The Gen7 1.3 page has it listed in the parts

Coil 100 uH | 1 | L1