Wow. Great project for your son. Excellent learning experience and your plan to keep the bike is spot on. The pride he gets everytime he hears it fire up in the garage will never fade. Looks like the bike is a good candidate as well.
How far do you plan on going with the engine? Clean and paint as is or are you going all the way in to the lower end?
+1 on Stev-o's comments regarding jets.
Main jets: The stock main jets on that bike were 110. With a less restrictive exhaust, you'll probably need to go up to 115-120.
Slow jets: Stock size on that bike is 35. If you keep a stock filter in your airbox, you shouldn't have to touch the slow jets but make sure you clean them good when you have the carbs apart. The slow jets are press fit on your carbs and don't unscrew easily like the earlier models. Grab them gently with a pair of pliers and give them a very slight twist to "crack the seal" then a small back and forth twisting motion to work them out. You have to remove them to get them clean. Don't worry about marring the outside of the jets as that won't hurt anything. Just don't grab them so hard that you crush them and change the opening. To replace, gently tap them back in with the handle of a screw driver or something that won't damage the top of the jet. If you put a less restrictive air filter in your airbox then you might need to up the slow jets to 38-40.
Needles: The needles on your carbs do not have the adjustment clip that earlier models had. Again, if you keep the stock filter setup, you shouldn't have to mess with the needle height but if you find that the bike runs lean in the mid throttle range, you can put a shim or two (small washer) in there to do that. There are a couple of threads on here with some pics and a good step by step on how to do that. If you can't find it, let me know. I have it bookmarked somewhere.
As Stev-o pointed out, there is no chart for jetting, but here is some good theory to get you started thinking about what is going on. Keep in mind that the different jets are related to throttle position and not your rpm or how fast you are going -
http://www.hondachopper.com/garage/carb_info/carb_info.htmllThere is a lot of good info regarding jetting on this forum but some not so good as well. Try not to get confused about the air/pilot adjustment screws (not to be confused with the idle adjust knob on the throttle linkage). On earlier carbs they were called "air" screws and they did just that - let in more or less air. Your PD carbs have "pilot" screws and they let in more or less fuel. So on your PD carbs, in is leaner and out is richer. The pre '77 carbs were the opposite (in richer, out leaner).
Have fun.