When rebuilding a 3s motor you will find that they are quite expensive to rebuild as aftermarket parts aren't as common as some other motors. In saying that they are available if your willing to spend the money. Oil pumps in the 3sgte are suppose to be better but I personally have never put one in a NA engine, during rebuilds I have only ever fitted them to the turbo engine they came from. I have always just used the genuine 3sge oil pump in the 3sge engine and have never had a problem with one. Unless of course the car has very high km's and that's a different story.
Water pumps are the same quailty/strength from one to the other so just get the one that suits the series of engine you have.
As far as weak points use some decent quality bearings (big end and main) and if you intend to give your car a hard time an engine oil cooler or larger sump maybe something to look into as most 3s engines seem to have oiling issues. Lots of further information on this can be found if you want to hunt around the different forums.
Rod bolts unless you have the money to spend I probably wouldn't bother as the standard setup is already strong. If you have no intention of using a turbo motor a set of camshafts would be a great idea as some reasonable performance can be gained by changing to various different cams. Just remember that the bigger the cam the more of a pig they are to drive around town.
If you are running the motor in rwd format I would suggest the Beams version, although more expensive they have much better power output and are much easy to mount North/South than the fwd counterpart.
I hope this helps
Aaron
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