As the eea resident i only supplied 3 months pay statements, my boss signed the form for me. and my wife received her RC

Yes

This route is still available i believe , but the ukba are yet to make a ruling after the recent European ruling was confirmed (Mcarthy), as it is free to apply nothing to loose, as soon as she gets to the uk send off the eea2 form as soon as possible,,

You can ask for all your documents back, they will forward the RC later, you have your COA,

I was told by immigration that if traveling together with EU resident then use EU channel, other wise use foreign passport queue, they do not stamp your passport in either queue

where did you read this, the UKBA website makes no reference to this, as i understand, it is on hold as there have been a number of legal challenges, to this proposal.