MR2QIK
This whole concept of "building it right" can get you in a lot of trouble. It's kind of a false illusion IMO since modified cars will never match Toyota factory reliability (not talking power of course).
My proposal.....fit the Beams with a manual tranny (good start...lol), Haltech ECU with flex sensor, injectors, pump, intake headers & exhaust & get a good tuner involved. I see no reason it won't hold up & it should provide lotsa fun. Bit of a Honda hunter....
I agreewith MR2QIK, you will see far more bang for buck with bolt on work. These engines are pretty restrained tune wise, and just getting them to breath better can be very rewarding.
I don't agree about a race motor beams does not require to retain VVT. BTCC cars, TRD touge cars, and some of the most powerful beams motors in the country including the winner of this years under 2 litre sport sedan all retain the VVT (in reduced cam throw) to help iron out any dips in the power delivery.

Unless your trying to build your engine to this kind of level, i wouldn't bother touching the internals.

When you get the upper end for n/a beams the power, even the diameter can effect power delivery, these three runs were just adjusting the diameter of the secondaries by 1/8th of an inch at a time.
Long story short, your best doing basics and tuning the engine to get the most out of it, it will be more reliable, better bang for buck, and will make the engine still suitable for street use.