When an implementation project for a standard system like SAP or Oracle E-Business Suite runs completely off the rails, it’s because the programmers have been allowed into the project.
Programmers are very accommodating people and they don’t like to say no. And true enough, given enough time and money, they can build anything.
The problem is that the business case for a standard system rests on the word “standard”. Not “almost-standard-with-a-little-bit-of-code”. By all means use the customization features built into the standard system to adapt it to your organization. But you allow even a little bit of custom code into your project, you are ripping out the foundation on which the entire business case rests.