Seasonal road bike tune-up: diagnose chain rub, crank-clicks, and tool needs

[PenelopeW]

I've been riding my aluminum road bike for daily commuting and weekend fitness rides for about two years now, and I'm starting to notice some persistent issues like a slight chain rub in certain gears and a subtle clicking sound from the crank area when I put down power. I do basic cleaning and lube my chain regularly, but I feel my road bike maintenance knowledge is lacking when it comes to diagnosing and adjusting the derailleurs, checking bottom bracket wear, or knowing when it's time to replace the cassette and chainrings versus just the chain. For seasoned cyclists who do their own wrenching, what is a logical order of operations for a thorough seasonal tune-up, and what are the essential specialized tools I should invest in first to handle these adjustments correctly at home? I want to keep this bike running smoothly for years.