The dirt road from San Manuel de Colohete [1] to San Sebastián, another attractive village farther west around Celaque, is not too bad, although there is a deep river crossing. Simple accommodations are available at a no-name hospedaje for US$1.50 a night, and Comedor Alicia on the square has meals (and also a couple of basic rooms).
If no ride is available, walk the road in 3–4 hours, and from there, you can continue walking several more hours on a remnant of the old camino real to Belén Gualcho [2], where you can spend the night and catch a ride the next day to Santa Rosa de Copán [3].
One bus a day runs between San Sebastián and Gracias [4], leaving San Sebastián at 5 a.m.
South of San Sebastián, the adventurous can hike down to Tomalá through lovely, little-visited, and safe countryside in southern Lempira, near the border with El Salvador. Locals say the mostly downhill route can be hiked in 10 hours, but more likely it would require camping out one night.
From Tomalá, transportation is available to San Marcos Caiquín [5] and on to Santa Rosa de Copán [3] or Nueva Ocotepeque [6]. Guides can be found in San Sebastián who know the way.
Links:
[1] http://www.moon.com/destinations/honduras/western-honduras/gracias-and-the-lenca-highlands/lenca-villages-south-gracias/san-manuel-de-colohete
[2] http://www.moon.com/destinations/honduras/western-honduras/santa-rosa-de-copan/sights/belen-gualcho
[3] http://www.moon.com/destinations/honduras/western-honduras/santa-rosa-de-copan
[4] http://www.moon.com/destinations/honduras/western-honduras/gracias-and-the-lenca-highlands/gracias
[5] http://www.moon.com/destinations/honduras/western-honduras/gracias-and-the-lenca-highlands/lenca-villages-south-gracias/san-marcos-caiquin
[6] http://www.moon.com/destinations/honduras/western-honduras/nueva-ocotepeque