On your point #3. Actually, you are incorrect. Profit is revenue - all costs. Whether or not it counts as COGS is only relevant for gross margin, a metric which isn't the best to judge software companies. R&D is an expense, so it affects your profitability and your net margin. If your company spends $100 less, that's $100 more you have in the bank, $100 less that you need to sell people on.
gross margin is unquestionably the metric used to gauge software companies. That's why we are so scalable. Especially SaaS. It's because our COGS are typically so low that we can afford relatively large R&D budgets (compared to other industries).
Lots of software companies have gross margin's north of 60% or even 80% (GOOG, afaik) which is unheard of in other industries.
If you focus your business on growing revenue and having a reasonable gross profit margin, you are focusing on the right knobs. If you are focusing on decreasing R&D as a means of maximizing net profit, you are focused on the wrong things.
http://www.investopedia.com/terms/g/grossmargin.asp http://www.investopedia.com/terms/n/net_margin.asp