What is the toughest implementation factor when trying implement an open source based technology such as an Open Source ERP ?

Reliable communications infrastructure and a backup plan for communications problems and ensuring information security and privacy and varifiable ability to detect and breaches as they take place (if that is doable today).

You have to test every function and make sure they are working correctly, open source solution is not formally tested, and when you found such issue you need to fix it and fixing it is done by two ways:

1)      There may be update that solves this issue.

2)      You need to fix it manually from the source code. 

Have cost effective access to consultuncy and trainng expertise to support you team to implement the ERP successfully to meet your specifications and a trusted party to implement any required customizations.

On the long run you have to develop your in-house skills to support the system and modefy it as required by changes in your business or in the technology or rely on a third party to provide such services.