Since I seem to be your enabler
I'll give a go to your questions; others will no doubt chime in.
1. Yes, you can use the online tool, many do so. You will see a number of alternative approaches mentioned here because of long-standing and, sadly, unresolved "bugs" in the online tool that actually have their
own thread here. In some cases, the online tool balks at itineraries where the first carrier is more recent, e.g. Qatar, or in some cases where the first carrier has authorized a different airline to do the issuing on their behalf, e.g. AA on behalf of RJ. Yet in other cases, the "bugs" result in mis-pricing, for example when one tries to use the rule that allows ending in a different African country than the origin, the tool prices the ticket as if the last country's price is the controlling one, not the first. Some airlines (e.g. QR again) don't reliably turn up as having availability when using the tool. And so on. Repeated attempts (by me and a number of others) to communicate with Oneworld to have them work on bugs in the tool have been met with silence. It's ironic - IMO the Oneworld Explorer is by far the superior product to anything Star Alliance offers, but Star's online RTW and related products' booking tool is vastly superior.
Try the tool to see; if it validates your route and gets you to the pricing screens (you can still bail) you're good to go. If not, since you're located in the US, you can contact the AA RTW desk at (800) 247-3247 and have them queue the fare to an issuing agency, e.g. AA in Japan, or Emeco in Cairo, or Mindpearl in Cape Town, etc.
2. Generally the ticketing airline is the first airline used, but there are some exceptions. Often you'll see people trying to avoid using BA as the issuing carrier because of BA's habit of adding huge fuel/"carrier-imposed" surcharges on other airlines' flights. Personally I always try to have AA as the issuing airline because their RTW desk (above) is very efficient at ticket changes, problem resolution etc., once you're underway.
3. If you're buying a DONEx availability isn't often an issue; airlines don't discriminate between one D-class ticket (a high-bucket business fare) as part of an RTW ticket v. a D-class ticket bought over the counter. I would not be concerned about availability in general. But see below regarding changes and re-issues.
4. Date changes are free; more substantial changes (e.g. change of route, change from transit to stopover) require the ticket to be re-issued ($125 plus any difference in taxes/fees.) So if you're planning to hold the ticket longer than the current booking window is valid (11/12 months etc.) you just put in "dummy" dates for the segments that aren't available yet, then change them once the "real" date opens.
5. Those are the current cheapest base prices. A couple of other origins, e.g. Jordan, Israel, Namibia, are not too much more, and one must always be mindful not only of the "positioning" costs entailed to getting to and from the origin points before and after, but also if a given origin point locks you into a "first carrier" that will impose excessive fees to the ticket. For example, originating in South Africa and heading to London as your first destination will stick you with BA as the issuing carrier, which will bring along BA's fees. The best thing to do is use the online tool to do some comparison shopping to see the bottom line inclusive of fees and taxes, add in your positioning costs, and go from there.
6. No, two stopovers in the continent of origin is the rule. In the case of Asia, look at opportunities for cheap "add on" tickets outside the RTW, e.g. a stopover in Bangkok will put you in a good place for cheap tickets to other SE Asian cities using local carriers at not much cost. Or put another way, use the RTW ticket for expensive segments, use the train or another mode for short hops where one of your 16 RTW flights would be overkill.
Download and study a copy of the rules from Oneworld
here.
Hope this helps.