Welcome, and first do not unbolt any crank/cam/valvetrain parts until the engine is at TDC. There is a tool for that in the kit, get it close to TDC first, and keep it near TDC as you do the work.
The hardest parts will be dealing with the balancer(removal), and loosening/tightening the bolts for the balancer and jackshaft. A second person and/or special tools to hold the engine still would help a lot.
The timing is as you noted very different. What is done is the crank(shortblock) is set to TDC, the cams are disconnected(cams move on their own, thus TDC is critical). Then one cam is held at TDC by a tool on one end, and the cam gear is held true(straight, cannot fall off) by another tool on the other end.
The jackshaft chain and gears and tensioners have to be done/replaced before the timing is set, those connect the cams to the crank. With the tool holding the cam gear true, that's when the cam bolt holding the gear to the cam can be loosened. The tool used for setting the cam at TDC only goes on in one way(out of 360 degrees etc.).
So you do the TDC, the jackshaft items, then the cassette, then the timing. If the engine was properly worked on with it at TDC to begin with, the cam will be near TDC. You simply use the cam gear to move the cam(and crank etc.) to its TDC(the cam tool). Then you will be loosening that cam bolt to move the crank back to exactly TDC, thus making them timed(tighten the cam bolt). The second camshaft is timed in the same way, the tools work on the two ends of each cam, in turn.
Remember to start with it all at TDC(crank), then as you do something which moves the crank from its TDC, move it back after each step. It's okay for it to get moved a little as you loosen the crank bolt for the balancer, just be sure to move it back promptly. When the cams are unbolted, that's when it's critical for the crank to be at TDC.
Let me know if that makes more sense than how it is in shop manuals. Good luck,