You seem to be working very hard.  I have only had the chance to run 303 so far.
At present I am finishing up a project that is supposed to be done by Feb. 1.  
At that time I'll get back to Madrigals.  Yes, you can delete the 2XX series of
of files.

It would be possible to put in automatic features for footnote numbers and 
accidentals in parentheses as you suggested but I won't have time for this 
at present.  Meanwhile there is a feature that you could use that may not 
be in your manual.  This is CP (= center by position of note).  For example 
if you wanted a natural in parentheses in front of the 7th note on staff 2, 
and that note is an A (p4=6) you would type as follows:

		   P1       P2       P3           P4        P5
  3 2 0 6 107 	<code #3, staff 2, horiz.pos=0, vert.=6, code # for (nat.)
  I		< go into edit mode for this item
  CP 7		< center according to position of 7th note on that staff
  X		< exit from edit mode
 
	(Of course this must follow input of all notes for this file.)
 
Then for footnote number 3 above the 10th note on staff 4:

 		   P1       P2      P3        P4       P5
  10 4 0 13 3	<code #10, stf.4, horiz.=0, vert.=13, the number is 3
  I		< enter edit mode for this item
  CP 10		< center according to position of 10th note
  X		< exit edit mode