Welcome to Flyer Talk
sc597 
Well done on the research to date. First up your RTW would be a DONE4 not a DONE3 - every continent touched counts (so Europe, South America, South-West Pacific, and Asia makes 4).
If you want to visit PPT, consider a Global Explorer (mileage based RTW) instead - the QF codeshare on TN is allowed on that. Alternatively you might want to use a separate ticket (perhaps an award) to get between south america and PPT and back.
Land segments don't count towards your 20 allowed flights, but both ends count towards stopovers.
Multi-leg flights that involve changes in flight number are counted separately. If it has only one flight number, and you aren't stopping over at the transit point, then it counts as only one segment. Eg SYD to LHR on BA16 is one flight segment, unless you stop over in SIN for a day or more, in which case it will be 2 flight segments.
JAL is joining OW in 2007. Once it has joined then may include on xONEx. Otherwise not allowed, even code shares.
You can buy a xONEx from any OW airline or any travel agent. If done via a travel agent they will pass the itinerary on to one of the airlines for pricing and confirmation it meets all the rules.
If you are intending a lot of travel and want to return home part-way through the year then 2 RTWs may make sense. Best to find a cheap country (not continent) to issue the 2nd one from - eg Sri Lanka and Thailand are popular amongst FTers. However you can still break the trip up by other means, eg an award or cheap paid ticket nested within the RTW.
On most flights discounted business/first class should be available 1 month or more ahead. However, some routes sell out of discounted classes a long way in advance. SCL-AKL is one such route where availability can be tough, especially in first (or even in business). Best to be flexible with dates. If your RTW included north america (would need to be DONE5) then you could consider travelling between south america and Australia/NZ via US (either as first visit to north america or by taking advantage of the south america transit exception).