There were some issues in the setRX and setTX functions for T4,x

It never came up much with T4 as there were not really alternative pins...

But fixed and tested with simple sketch on T4.1 and simple jumper to TX and RX pins on memory chip locations

teensy4/HardwareSerial.cpp

 {
 	if (pin != hardware->rx_pins[rx_pin_index_].pin) {
 		for (uint8_t rx_pin_new_index = 0; rx_pin_new_index < cnt_rx_pins; rx_pin_new_index++) {
-			if (pin == hardware->rx_pins[rx_pin_index_].pin) {
+			if (pin == hardware->rx_pins[rx_pin_new_index].pin) {
 				// new pin - so lets maybe reset the old pin to INPUT? and then set new pin parameters
+				// only change IO pins if done after begin has been called. 
+				if ((hardware->ccm_register & hardware->ccm_value)) {
 				*(portConfigRegister(hardware->rx_pins[rx_pin_index_].pin)) = 5;
 
 				// now set new pin info.
+					*(portControlRegister(hardware->rx_pins[rx_pin_new_index].pin)) =  IOMUXC_PAD_DSE(7) | IOMUXC_PAD_PKE | IOMUXC_PAD_PUE | IOMUXC_PAD_PUS(3) | IOMUXC_PAD_HYS;;
+					*(portConfigRegister(hardware->rx_pins[rx_pin_new_index].pin)) = hardware->rx_pins[rx_pin_new_index].mux_val;
+					if (hardware->rx_pins[rx_pin_new_index].select_input_register) {
+					 	*(hardware->rx_pins[rx_pin_new_index].select_input_register) =  hardware->rx_pins[rx_pin_new_index].select_val;		
+					}
+				}		
 				rx_pin_index_ = rx_pin_new_index;
-				*(portControlRegister(hardware->rx_pins[rx_pin_index_].pin)) =  IOMUXC_PAD_DSE(7) | IOMUXC_PAD_PKE | IOMUXC_PAD_PUE | IOMUXC_PAD_PUS(3) | IOMUXC_PAD_HYS;;
-				*(portConfigRegister(hardware->rx_pins[rx_pin_index_].pin)) = hardware->rx_pins[rx_pin_index_].mux_val;
-				if (hardware->rx_pins[rx_pin_index_].select_input_register) {
-				 	*(hardware->rx_pins[rx_pin_index_].select_input_register) =  hardware->rx_pins[rx_pin_index_].select_val;		
-				}	
 				break;
 			}
 		}
 
 	if (pin != hardware->tx_pins[tx_pin_index_].pin) {
 		for (tx_pin_new_index = 0; tx_pin_new_index < cnt_tx_pins; tx_pin_new_index++) {
-			if (pin == hardware->tx_pins[tx_pin_index_].pin) {
+			if (pin == hardware->tx_pins[tx_pin_new_index].pin) {
 				break;
 			}
 		}
 
 	// turn on or off opendrain mode.
 	// new pin - so lets maybe reset the old pin to INPUT? and then set new pin parameters
+	if ((hardware->ccm_register & hardware->ccm_value)) {  // only do if we are already active. 
 	if (tx_pin_new_index != tx_pin_index_) {
 		*(portConfigRegister(hardware->tx_pins[tx_pin_index_].pin)) = 5;
 	
 		*(portConfigRegister(hardware->tx_pins[tx_pin_new_index].pin)) = hardware->tx_pins[tx_pin_new_index].mux_val;
 	}
-
+	}
 	// now set new pin info.
 	tx_pin_index_ = tx_pin_new_index;
 	if (opendrain)