You might want to verify your furnace but I've not seen an air handler with strip heaters that requires a neutral. The control transformer primary and blower motor are 240V . If this is accurate for yours, you can use 6/2. Have you considered taking the advice of nunya
about running conduit the entire length of the circuit and using THHN/THWN? It would allow smaller conduit, be much easier to pull, eliminate the questions that surround the compliance of cable in conduit and probably be less expensive.
The AHJ here won't allow stripping the sheath off of the cable for use in conduit. Of course, they have to catch it but most local inspectors can tell the difference between a THHN conductor that was manufactured as a single conductor and one that was cabled. Their argument is the cable was approved and listed for a particular use as it was originally manufactured and stripping the sheath for use in conduit is an unauthorized modification and thus renders it unlisted and in violation of 110.3(B)
Of course, YMMV 110.3(B) Installation and Use. Listed and labeled equipment shall be installed and used in accordance with any instructions included in the listing or labeling. --