First you have to realize that many sorts of documents were made for different purposes.
Second, a lot of records do not survive - due to exigencies of war and due to fires in Washington that destroyed a great many records, such as muster rolls and pay rolls.
Third, even within the main listings of Continental Troops (see below), a great many documents were not indexed at all or faultily indexed.
The receipt mentioned may have been submitted to the Mass. General Court or to the Committee of Correspondence/Safety for reimbursement as part of a list of payments made.
Such a receipt roll did not necessarily survive among Regimental records obtained by and microfilmed by the National Archives.
You may have searched existing indexes to National Archives Micropublication M246, "Revolutionary War Rolls" and found many persons named William Cook but not specified as part of Nixon's Regiment.Indeed there appears to be no separate listing for this Regiment in the National Archives as such, see the brief listing by roll number of what is on each microfilm roll (thanks to John K. Robertson and Bob McDonald): http://www.revwar75.com/ob/m246.htmhttp://www.revwar75.com/ob/m246.htm
However, F. B. Heitman's _Register of Officers of the Continental Army_ gives a little more information about where Col. Nixon and Capt. McFarland were in the course of the War:
Nixon, John (Mass). Captain Company of Minute Men at Lexington, 19th April, 1775; Colonel of a Massachusetts Regiment, 24th April to December, 1775; wounded at Bunker Hill, 17th June, 1775; Colonel 4th Continental Infantry, 1st January, 1776; Brigadier-General Continental Army, 9th August, 1776; resigned 12th September, 1780. (Died 24th March, 1815.)
McFarland, Moses (Mass). Captain of Nixon's Massachusetts Regiment, May to December, 1775; wounded at Bunker Hill, 17th June, 1775; Captain 4th Continental Infantry, 1st January to 31st December, 1776; Captain 6th Massachusetts, 1st January, 1777; transferred to Invalid Regiment, 16th March, 1779, and served to close of war; Brevet Major, 30th September, 1783.
However, you do not say if a Regiment, Captain or other officer was identified in the later entries for your man.
The above listing gives the microfilm roll on which there are some documents for the 4th Continental Infantry Regiment, which you can browse either by looking at the actual microfilm (you can order from the National Archives to look at through your local library's inter-library-loan service if you give them the micropublication number and title and roll number).
If the later listings for your man do not specify service with McFarland and Col/BrigGen Nixon, you have to do some detailed analysis to figure out what sort of document is referred to and whether it may survive as an item within a specific Regimental list.
The National Archives did not acquire most County Militia records, so if your man's listings in Mass. S&S refer to militia duty you would have to write to the Mass State Archives about what document they can search for and provide copies of.
You do not exactly quote the further items for your man, so I can not offer specific advice for the various entries.