The frequencies in question can be changed only by modifying RCW fields - refer to the QorIQ T4240 Reference Manual, Figure 4-2. T4240 logic clock subsystem block diagram-cluster group A and Figure 4-3. T4240 logic clock subsystem block diagram-cluster group B.
Pre-built RCW images for T4240RDB could be found in the QorIQ Linux SDK v2.0 PPCE6500 IMAGE ISO available for free at:
https://nxp.flexnetoperations.com/control/frse/download?agree=Accept&element=7726177
The T4240RDB RCW update procedure is described in the QorIQ SDK 2.0 Documentation, 4.4.17.8 Programming a New U-boot, RCW, FMan Microcode:
https://www.nxp.com/docs/en/supporting-information/QORIQ-SDK-2.0-IC-REV0.pdf
Custom RCW could be prepared using CodeWarrior QorIQ Configuration and Validation Suite PBL Tool:
https://www.nxp.com/docs/en/user-guide/QCVS_PBL_User_Guide.pdf