1) As Chris says, because you had a whitley grading appeal in place before AFC the outcome of this appeal must be backdated to the date it was filed. Therefore in October 2004 it should be the mto3 band that is used to move across to band 6. This still won't result in pay protection but may shift you up an increment or so.
2)From the Q&A of the NHS employers website
"Do staff continue to receive pay increments on their Whitley basic pay past 1 October and 1 December 2004 and until they are assimilated to Agenda for Change pay?
Section 46, paragraph 9
Yes - and the basic pay on the effective assimilation date is to be calculated as in paragraph 46.9."
Section 46 paragraph 9 is :-
"An employee’s current pay for the purpose of assimilation to the new pay spines and bands, referred to below as “basic pay before assimilation”, is their annual full-time equivalent basic pay on the effective assimilation date plus the annual value of any job evaluation related allowances (see Annex Q) plus the average value of any bonus payments under schemes which are discontinued (see paragraph 46.42 below)."
Now here is where it gets confusing: the "effective date" in the handbook is stated as being October 2004 BUT both the handbook and the Q&A infer that the "effective date" is the "actual" assimilation date and any increments earned on whitley should be taken into account. The Clincher on this argument is section 46 paragraph 20:-
"The level of pay before assimilation for the purpose of this calculation will be the average level of the payments in the left-hand column of Table 7 above over a reference period of twelve weeks or three months ending at the assimilation date except:
- where this period includes the annual pay award due in April 2005
or an annual increment, the protected amount should be adjusted as if that award or increment had applied throughout the reference period;"
Which shows that the assimilation date is NOT October 2004 but the ACTUAL date since it refers to 12 weeks including April 2005 (my handbook was written in January 2005 and expected afc assimilation to be finished by end of 2005

)
Now if you take this paragraph to the extreme you can argue that your current MTO3 increment must be used to work out your pay band in October 2004 and then work on from there

3) For protection purposes the date referred to is "assimilation date" NOT the "effective assimilation date" so I would argue strongly that protection starts at the date you are actually assimilated i.e. NOW and therefore if all the above fail you should still be on protected pay until October.
If you're in a Union make them earn their dues (ps if it's one of the 7 that accepted the pay deal after getting an overwhelming No vote from their members ask them WHY?)