I use online build threads like the one offered on stovebolt for historical reference. They become sort of a real-time testimonial to work done and work yet to be completed. I make notes (like engine numbers, parts numebrs, etc.) that help me when ordering parts or considering stuff on ebay.
Digital pictures with the date stamp are good for memory lapses.
I tried once to keep track of my time and money on a spreadsheet for my first car project but that just made me feel behind schedule and over budget.
I never thought of microsoft project for a car project - i'd be so far off "critical path"