Cowle(Cowll, cowell etc) + cowley are I think unrelated (at least in all 18th C wills/deeds etc I've looked) tho they may have common roots.
Brian normalised names - eg first names were expanded but often with an abbreviation it is easy to misread then the expanded name misleads searchers as you don't think that it could be misread - he made a significant mistake with Eliza only realising too late that it was distinct from Elizabeth - others to look out for are Richard/Robert + Christopher/Christian.

I'm not sure there is an easy solution - what do you do with Quay/Kay, Juke/Duke etc, (or vinch/finch etc - I've seen vargher is some early material) the Callister/Collister is common because in many hands the a and o are virtually the same.

I adopted a per parish listing for my will summaries etc so that you can quickly scan down a list of names