One problem related to manual transmission has been reported for the 2001 Dodge Ram 3500. The most recently reported issues are listed below.
Nv5600 6 speed transmission has severe gear clash in third and fourth gears. Will not down shift into third gear with gear grinding. Trouble started about 1 month ago, at 92, 000 miles. Dealer tells me that parts are not available to repair and they are not sure if Dodge is having a problem. TSB 21-009-01 indicates Dodge knew of problems in 01, but have not done much since then.