I have previously used confocal microscopy on hyphae and ascocarps of Thelebolus and Sordaria. For cell wall staining try the FITC conjugated lectins Concanavalin A (specific for manans/glucans) or Wheat Germ Agglutinin (specific for chitin) available through SIGMA.
For a comprehensive review of other probes used in confocal microscopy for fungal samples see: Czymmek, Whallon and Klomparens. 1994. Confocal Microscopy in Mycological Research. Experimental Mycology 18: 275-293. Please feel free to contact me if you have any direct questions.

Kirk J. Czymmek, Ph.D......email:kirk@noran.com