Disassemble . You'll have allot of bike apart just to get the engine out.
Do you have an impact screwdriver for those stubborn case and head screws? Harbor Freight has them cheap but the bits are crap, NAPA is expensive, some of the other auto parts stores may have a decent one at a reasonable price. see if they sell bits separately for later on, you 'll need them ( the big Phillips head). also ,some come in 3/8"drive and some are 1/2" drive, it only matters if you want to use it with your impact sockets.
Ziplock freezer bags and a good marker to id pieces, take pictures as you remove parts, so you know how it's supposed to look as you reassemble and we can watch your progress.
What do you want to tackle first, engine or everything else? You can remove the top end and find out what's going on, it'll make it lighter for removal. Rebuild it so you know it's all good then either stuff it back in the frame and keep it original (then you could ride it )or go all out on the rest of it (takes time+ $ from the family), Your little guys won't be little guys long, you may want to plan a father and sons restoration when they get to the defiant age, where they need more of your time and attention, but don't know how to ask for it. They will have lifelong memories of building these machines with Dad, and appreciate them.
Get them interested in the engine , then the ride, the rebuilds as they get older. Double legacy. You 're a good Dad.