One of the difficulties (or perhaps, 'opportunities' - ugh!) of depicting ECW units as they might have appeared in battle is that most of the regiments were usually under-strength and tended to be grouped into brigades (or tertia), without knowing which regiment provided what proportion. Your plan to paint the figures in a mixture of colours based on the probable/possible coat colours of the contributing units, with the fall-back option of grey/red for parliamentarians or red/blue for royalists seems right.
Also, I am not sure whether each brigade was deployed as a single block or as two or three blocks. From what I have read of
First Newbury, it seems that most of the regiments (and contingents from regiments) were amalgamated as brigades. For example
Skippon's brigade in Essex's army, if we assume that it consisted of Skippon's, Bulstrode's and Brooke's regiments, and totalled 1,050 men, was it deployed as a single block of pikes flanked by two shot 'sleeves', or was it two or three blocks of shot/pike/shot? I would suggest that as the 'ideal' foot regiment of the time was of 1,000 men, then it would have been one block. However, would
Belsyse's brigade of 1,800 men in the Royal army have been one block or two or even three? I suppose it should depend on your own feeling from what you have read and what looks right on the table-top, depending on what man to figure ratio you are using.
In my list of foot units, I should have pointed out that from the sources (sounds a bit grand, when in fact I mean books from the library) I have read that the London units, i.e. the trained bands, the auxiliaries, with Mainwaring's and Springate's, seem to have operated as separate regiments.
I probably should get out more...
PS - What figures are you using?