We highly recommend the use of an oscilloscope to debug the timing, especially for the medium access control layer. We have been using the Tektronix MSO2024 with the DPO2EMBB and the DPO2COMP extensions. This oscilloscope features a 16 channel digital probe which is able to decode I2C, SPI and UART (three communication protocols that chips on the boards use to communicate together).
Another interesting tool is a spectrum analyzer, to identify on which frequency motes are communicating, and to detected the presence of interference. The figure above shows a typical setup.