Jablanica-Konjic Tunnel

Whatever your plans are: Avoid the route from Sarajevo to Mostar (and even more so in the other direction). It is sheer hell for cyclists, with lots of traffic and ruthless truck drivers. Unfortunately, taking a train is no alternative since they don't transport bikes (I haven't tried it, though).

You can put the bike on trains (i did). There are busses and you can put the bike on them as long as they have enough room for it. Anyway if you want to cycle between Mostar and Sarajevo just go via Rujiste and from konjic the street will be wide and around 10 km after that there will be less traffic (highway starts near bradina) and go for the Ivan sedlo pass (not steep and no traffic) to avoid the tunnel. Or from konjic take the mountain and go for the bjielašnica pass. Additional info: on rujiste you will find no water the whole way from Mostar to konjic, take plenty with you.

This tunnel is very unpleasant and there isn't enough pavement to walk on. Cycling is the only option. In hindsight I'd probably just get a taxi from Jablenica to Konjic as the road is very busy and feels very dangerous.