Bars, seat, and footpegs. Where they should be is up to the individual, and opinions vary wildly of course. I'd guess I have scratch - built somewhere between 20 and 30 "rear sets" and hopefully have learned a bit about making them.
For me, the most important thing is to not lose sight of how critical all three things are determine all at once - the bars, seat and pegs are all one project for me - building one element without having at least a mock up of the others in place does not make sense to me. The driver is the other critical component since everyone is a different size and has different preferences.
I suggest that you mock up your expected seat height and then try out your peg location. Then keep adjusting until you get everything just right. The seat height usually seems to turn out to be the hardest to adjust, so make your best guess at that and mock it up so you can sit on it. Adjust your chassis so it is at the expected ride height with your best guess at suspension sag. Once you get a set of pegs tacked up (or clamped up , or even held up by wood blocks!), you can sit on it and get an idea of where you want the bars and pegs to go. For me, I spend a lot of time fooling around with the bars and then the pegs going back and forth changing them until I home in on exactly the right thing. The last guy I built a bike for definitely got impatient by the third visit to my shop getting his new bike "fitted" to him, but it paid in the end as he tells me practically every time I see him how comfortable and easy to ride his new bike is.
I don't have much in the way of "rules of thumb", but I will say that for rideability, pegs should be lower and farther forward and the bars should be higher than on a road race bike. Clip-ons are cool and fun but a lot of work on the street (I have them on one of my own bikes), and likewise with race location pegs (also on the same bike). Clip on bars vary quite a bit depending on the bike as to how high they are. The seat height is critical - bars at (like my bike) or below seat height are race bike territory, but on many bikes they can be a bit above seat height and be vastly more practical. The pegs on that bike are even with the swingarm pivot bolt and about 6" back. They are plenty high, at least from a scrape in cornering perspective (that includes the foot brake arm when depressed and my boot). I have long legs - an important factor. I love this bike and it is a blast to ride - for about 20 minutes - after that I start thinking about how far away from the barn I am.
Mock up the seat, bars, and pegs, and then sit on your bike, put your feet on the pegs, and grip the bars. Remain that way for 15 minutes - that would be a VERY short ride. After that, if you are confident you think it is perfect, start welding! Otherwise, adjust and repeat. I urge you to spend some time doing this, you likely can't make a good judgement hopping on your mock up for 2 minutes and thinking "that feels ok". See if you still say that after 15 minutes. 1" on the position of anything can make ALL the difference! Next year when you are riding it around, you will think it time well spent!
Going to be a beautiful bike - it should be as great to drive as it is to look at!