Can you please confirm that the MPC8541 ethernet input clock is actually 2 clocks: one for each eTSEC, with name TSECn_GTX_CLK125/GPIOm? The MPC8541 ballmap spreadsheet only shows one gtx_clk125 pin (like the 8536), but the current data sheet (Revision E) indicates there are two.
The ball map shows only primary functions of a pin. By default both the eTSECs would share the same clock i.e TSEC1_GTX_CLK125 @Y29. If required, user can opt to use separate clock for eTSEC2. The separate clock for eTSEC2 is multiplexed with TSEC_1588_TRIG_IN1@AH27 and can be configured using PMUXCR[6:7].