I just made this trip. Paid a tiny bit more (booked a few weeks ago), but booked it with a 4 night stopover Tokyo. (I also had to pay $20 for the call center ticket since I couldn't get the website to book the 5 hour turn in CGK) Great trip little trip and JAL has a pretty good PE product IMO. (although if I wasn't doing this to finish out EXP, I don't know if I would have paid the premium for PE it since their economy seats are pretty good on the 777-300ER and 787s.) My trip was:
5 Oct - CMH-ORD (H) ORD-NRT (E) - I needed to be in Tokyo for Wednesday through Friday
10 Oct - NRT-CGK (E) CGK-NRT (E)
11 Oct - NRT-ORD (E) ORD-CMH (H)
I did the 5 hour turn at CGK. As far as I am concerned there is little reason to stay in Jakarta. Jakarta is pretty hazy (with the burns going on), polluted, and extremely congested - and the place isn't the cleanest or easiest place even on a good day. I had to explain why I was spending only 5 hours in Indonesia to the immigration officers (which was not as easy as it normally has been) and involved the first officer calling over another to question me about what I was doing. (I normally don't mention miles runs or anything of the sort, but when I mentioned it to the second officer, he seemed to understand and told the first to let it go - Just the luck of the draw I guess) I suppose I could have gone to the transfer desk, but wanted to park myself in the Ibis for a few hours to take a nap and shower. JAL is currently putting PE passengers in the JAS lounge, which isn't too bad, but the one shower stall in the place is pretty grungy. (IMHO) - The budget Ibis isn't that great either, but for a taxi ride and ~$20 for the room, it is much more comfortable than the hot terminal at CGK. (if you don't need a shower or sleep, you might consider just staying airside and going to the lounge after getting your ticket and stamp, if you have the option.)
Overall, a very doable trip for a miles run and adding the CGK leg actually reduced the cost of the flight to Tokyo for me. (I personally find long legs are easier since I seem to be OK once I settle into a seat - and this one has a 13, 11, and two 8 hour legs) I should earn ~29,068 EQP and ~52,796 RDM with the PLAT bonus and the Asia RT bonus promo. (Be forewarned that the miles don't post for at least a few days if you purchased on JAL stock. My 5 October miles just posted this morning (12 October).) Not the most economical miles/points run, but for going to Tokyo anyway, this is a pretty good option.