This was meant to be a simple product from the beginning, but from the beginning it was clear that no manufacturing project is ever "simple".

I believe I mentioned this before. For the sake of organization you want the Manufacturing BOM separate from the Electronics BOM, but certainly, they live the same life. We may have planned everything smoothly for all the manufacturing, tool-making, etc, just to get a notification like this:

We do not want a notification like this. 

This is when services such as Findchips come in handy (Full disclosure, both DesignLab and Findchips are owned by Supplyframe Inc.). I am a Product Designer so I do not make the most of the service, but Erika does and that is really cool.

One of the tools that I use a lot is a Project Management application called Project Libre (https://www.projectlibre.com). It is a simplified version of Microsoft Project without the price tag. The biggest drawback would be the fact that it is difficult to share the information with anyone who does not have the software (along with a few glitches here and there), which could be an advantage if you look at it from a different perspective :)

I have tried creating complicated spreadsheets in Google or Excel together with Gantt charts, but I quickly end up missing the degree of control that you can have with a project management tool. Being able to select who works what days, how many hours, what tasks begin before, after, concurrently in relation to other ones, etc., are just a few things that you could have with a spreadsheet but would take a loong time.  If you want to estimate with some decent accuracy how long a project will take, I would say this is the way to go.