I would suggest looking at pages 30 & 31 of the Beneteau 343 owners manual. There is a schematic with a layout of all of the deck organizers, turning blocks, and clutches / jammers for each line. There is a dedicated clutch for the main halyard; therefore, you should not have to remove or switch liines to release the main halyard. If your furler is working well, I would mark the main halyard posiition as it runs through the clutch so you can reset to the same position when you rehoist the main. Note that there is quite a bit of tension on the main halyard when it is properly set. As was mentioned by others, look at the mainsail luff for vertical wrinkles (halyard too tight) or horizontal wrinkles (halyard too loose). There is only a very small range of 2-3 inches for the halyard to be too tight or too loose. I can't overemphasize that if the furler is working smoothly with the present halyard tension, mark the halyard as it travels through the clutch and reset it at the exact mark when you rehoist the main sail to save yourself a lot of trouble!
I would also recommend checking out the Neilpryde Sails website for the "Sail Trimming Guide for the Beneteau 343" and the US Spars website for operation and maintenance of the mainsail furler and tunning the rig.