Assuming that you could gather the facilities and political will to start a Javan rhino breeding program, how would you do it?
I am not sure I or anybody else truly knows SE Asia, even Asians themselves

Your question:
- Establish as group of 3-4 zoos in Europe or USA experienced in breeding Indian rhinos and set facilities. They can be used for other rhinos if the Javan rhino program fails.
- Check if health and reproductive status of rhinos can be checked before export using eg. portable ultrasonographs. No point in exporting sick or elderly rhinos.
- Using tracking to find juvenile or young rhinos and dart them with tranquilizer guns. More difficult than pits, but poachers can shoot rhinos using normal guns, not?
- Export 4-5 rhinos to fine tune husbandry.
- If everything goes well, export 10-15 rhinos within 5 year period.
Cost is in ten millions of dollars, but this is a cost of one major zoo exhibit.
What I wouldn't do:
- Start new breeding centre in Indonesia. Sorry, but breeding centres in tropical countries usually have big problems with security, untrained staff, organization, hygiene, funding etc. Compare sumatran rhino centres. This doesn’t compensate for advantages of local climate and transport.
- Assume that javan rhino needs extremely big enclosure, space etc. They most likely like Indian rhino breed in what can be called good-standard zoo.
I know it is impossible for political and social reasons. Government would not export animals, even if they go extinct, field workers hate zoos, there is no coordination between parties, people feel that doing nothing is politically safer than risk taking etc. But you asked what should be done if human problems did not exist.
Also, I remind with problem of Ujung Kulon:
- Reserve is thick forest, marginal habitat for grazing rhino,
- Habitat gets worse as the forest matures
- Rhino population is at carrying capacity with no food to grow
- Rhino population of this size will go extinct purely from inbreeding.
- Rhinos will be forever vulnerable to disease at a single site
- Rhinos will be forever vulnerable to breakdown of security, eg. refugees
- Rhinos will be forever vulnerable to natural catastrophe like Krakatoa.
All these problems were named 30? 40? years ago - and nothing was done.
Overall, I want to say, that protecting rhinos is also organization effort. You need your plan to fit not only biology and mythos of free nature, but also national and local security, organization, trained staff and funding. Not understanding will make rhinos extinct.
Everybody understands than you cannot keep gold under poor protection, because it will be stolen. Rhino horn costs more than its weight in gold. Nevertheless, well-meaning people try keeping rhinos in poorly protected reserves and cry with surprise when another rhino subspecies gone extinct.