It's been so long since I read that manual that I only remember it vaguely....
How much do you want to spend?
Some big improvements all around come from losing weight. Whether it's the engine or on the chassis.
Battery - smaller lighter modern battery (Odyssey?)
Alternator - smaller lighter modern (Kubota?)
Leaf springs - Carbon composite will drop a noticeable amount of weight
Shocks - Very good modern ones available
Ignition - Programmable dizzy or Crank fired ignition (affordable solutions are out there)
Header - Available headers are better than the stock manifold, but, a 4-2-1 header would be much better. Unfortunately you would have to have it built custom. If you go custom, take the time to have it reasonably specced to your engine - too big costs performance and weight penalties.
Exhaust - If it's not already, go to 1 3/4" (1600?) exhaust with good non-restrictive muffler.
Flywheel - If it's for the street, you might not want to go super light.
Engine
Oil - make sure you use a good oil with the proper ZDDP components - Oil grade is up to you, several discussion threads on the board.
Valves - A good 3-5 angle valve job and open the throat to 88-90%. Lighter valves will increase your rpm capability without having to increase spring pressure...to a point. At a certain performance level you may want to get a slightly larger exhaust valve (1600).
Pistons/Rods - The stock pieces are extremely heavy by modern standards. Modern equivalents are 1/2 the weight (part of the reason a U20 can't compete with the SR20). It is also very expensive to replace these parts with modern pieces. Lightening and prepping the stock rods according to the manual will help somewhat. Lighter rods/pistons also contribute to a smoother running engine with less stress on the bearings.
Cam - Modern grinds make a difference! Depending on your desired use spec the cam and compression ratio to work together.
Crankshaft - Removing the casting flash and smoothing the casting lines is about all I would do, other than addressing the oiling issue (if racing). I have read that lightening the crankshaft on a 4 cyl may have detrimental effects on longevity.
Vibration Damper - I'd recommend one for every engine, especially if pushing the performance level. It protects the crank, but also dampens the vibrational effects on the valvetrain.