Last Saturday I actually did the Bogor trip.^
Free shuttle from hotel to airport T2 (international). The Damri bus from the airport T2 "bus shelter" took about 90 minutes arriving at the station next to the Botani Mall and Gardens. Getting into the Gardens was an interesting exercise considering the non-stop traffic at the traffic circle. I survived but there is an easier way. Exit the station headed to the circle turning left, at the first street junction turn left headed up the street and use the underpass. Continue on the other side of the street in the same direction for another 400m or so. Entrance fee 25000 IDR.
I walked through the Gardens and was able to assist a couple of groups of (polite) teenagers with their English practice. The questions were very similar for both groups.
The following is not recommended if you are over 180cm. Local transport is handled by minivans. The emphasis is on MINI. You want to catch a route 03 which will (eventually) get you to the station. You will need to get into the single ticket line unless you already have the "commuter rail card". Elapsed time about 15 minutes (remember this is Saturday afternoon). The glitch to this is that the Damri buses leave from the Gambir station downtown to go back to the airport. Commuter trains no longer STOP at Gambir station.

The taxi fare from Juranda station (the next on the line) cost more than the train ticket. But was worth it as the rain started about the time i got there.
But there was a compensation in the end. I was staying at the Ibis Styles at the airport (entrance). It seems all the Damri airport buses stop there for some sort of security check and this saved me more than an hour travel time. Time from downtown to bus exit about 40 minutes.
Hope all of this helps you in your wandering
Fred