Concerning re-building the bottom end, you need to set your goals on what you want to do...an upgrade to the mid to high HP (400-500) numbers or leaning more modest close to stock HP (300-350). The turbo you choose will determine how stout a bottom end you need. Questions to ask yourself:
- How much $$$ do I want to spend

considering high HP is going to cost more $$$
- Which MHG to use? Cometic is good for most applications.
- Stock pistons or aftermarket? JE, Ross, Wisco...all good choices.
- Just a hone with stock pistons/oversize rings or bore it out for aftermarket.
- Stock rods? Usually good up to the 450 HP numbers....Eagle rods are good for most on the aftermarket side.
- Balance the rods & pistons?
- Turn/balance the crank or just micro polish the rod surfaces?
Regardless, you do want to have the crank checked out and use new bearings on the low side of Toyota spec for clearance. Replace crank/cam seals and timing belt with new. I feel a 3 angle valve job and replacing the valve seals is a must to do it right...measure and adjust the valve shims before you put the head on. The block and head will need to be decked to the RA spec for the MHG you chose.