Bolt-ons for the 1.3L ranked by my thoughts on best bang for buck & difficulty:
* CAI (only because it's so cheap & easy) or DIY snorkel
(read this first:
http://www.bobistheoilguy.com/index.php?option=com_content&view=article&id=58&Itemid=66)
* Modify or ditch the stock carb (this is BY FAR the most restrictive part of the engine, and carb mods can be done for 'free' with hand tools)
* Cat-back exhaust (2-2 1/4")
* High-flow cat
* Headers
* Cam (only if you want power higher or lower in the RPM range)
* Port matching (this could be higher on the list because it's so cheap to do, but the other work needs to be done before you'd see any real gains from it)
* Head work (machine shop high-flow magic)
* Under drive pulley & adjustable cam sprocket
The header can get some good gains, but it's not what I'd do first (I start with the most restrictive systems and work towards the least restrictive). The biggest restriction is the pipe size & stock exhaust can.
If you've got the tools & place to do the above bolt-ons, I don't see why you wouldn't have the resources to do an engine swap (I can rent engine pickers around here for a few $$$ a day). Calmini header alone is $260 + Tax + S&H. I see 22re's going for $500 (asking price, so they'll go lower) every few days between pirate, craigslist & other Toyota 4x4 boards. Just food for thought.