When you're severely downtuning, it's better to start with a strong, clear fundamental. Those low strings will have tons of overtones for you to work with, but to get clarity, you need to focus on getting a tight fundamental for the notes to be clearly defined.
If you're going down to F#, you might consider exotic woods that are more commonly used in bass construction, like wenge, bubinga, zebrano or walnut (or combinations thereof). You might also consider alder or swamp ash for a snappier tone. Woods that have more 'warmth' to them like mahogany or rosewood might soak up too much fundamental and leave you with nothing but mushy overtones to work with. Stick with hardwoods if you can, which tend to have stronger fundamentals.
As for electronics, either go with more vintage-voiced, medium output passive pickups to keep clarity and articulation on those ultra-low notes, or put in a set of EMG 707s. You can always add more gain to get more crunch, but if you've got an excessively loud and muddy signal coming from the strings and pickups, you'll have a much harder time getting good tone and articulation at the amp.