dont rush things... i know u're eager, i know u feel confident of ur skills or maybe u just wanna throw some money this one shot rather than spend again later..
either way im telling you:
for whatever u have so far, stay with it and get used to the stock settings first. give it at least another couple of months. troubleshoot slowly with the help of experienced mechanics on areas u should bring up to date first; as most of ur parts are still 2nd hand halfcut condition. get to know the car before it throws u off like a wild horse trying to be tamed.
be patient with the mods. ur money is more useful elsewhere for the moment. glad to know that u're happy with a newly done transplant but its not all about taking the "new" car out to thrash it out there to see how fast u can go. if u still choose to learn as u go the hard way & wont listen to someone who as made that mistake and paid for it now trying to help u avoid unnecessary problems/complications, i bid u good luck. i didnt & wont force u to do simply anything.
i agree with ur no. 2; u should at least just check ur voltage/amp/resistance/impedance settings for all sensory and electronic-controlled parts on ur engine such as TPS, Injectors, O2 sensors, Distributor etc to make sure they are working properly and/or within their proper range (as dictated in the factory manual) altho these things are hardly touched by japanese users unless the halfcut was a race-prepped car.
a copy of the 4AGE factory blacktop manual can be obtained here if u know who to ask. i urge u to learn the car/brakes and limits in a civilised manner for a few more months before thinking abt taking corners at top speeds and start modding.
have a good toyota experience! :)