How is the fuel pressure and the lambda values?
And no there isn't much you can do with the stock ecu to make it run richer. Losing the EGR creates a very lean condition in the mid range of the RPM and the ecu cannot compensate for it. Some people used bigger injectors or upped the fuel pressure but that opens a other box of problems.
The only way to run the engine properly without the EGR is to use aftermarket ECU.
