Index: firmware/source/sys_main.c
===================================================================
diff -u -reb877ae36c28eb83553ee11ccccf42e2c4a5b4d2 -rda054e07ed923d897e58f77a14e21d864ac4d5b8
--- firmware/source/sys_main.c	(.../sys_main.c)	(revision eb877ae36c28eb83553ee11ccccf42e2c4a5b4d2)
+++ firmware/source/sys_main.c	(.../sys_main.c)	(revision da054e07ed923d897e58f77a14e21d864ac4d5b8)
@@ -52,24 +52,34 @@
 /* USER CODE BEGIN (1) */
 #include "system.h"
 #include "sys_dma.h"
+#include "adc.h"
 #include "can.h"
+#include "etpwm.h"
 #include "gio.h"
 #include "mibspi.h"
 #include "sci.h"
 #include "rti.h"
 
 #include "Common.h"
 #include "AlarmLamp.h"
+#include "BloodFlow.h"
 #include "Buttons.h"
 #include "CommBuffers.h"
 #include "CPLD.h"
+#include "DialInFlow.h"
+#include "Dialysis.h"
 #include "FPGA.h"
+#include "InternalADC.h"
 #include "MsgQueues.h"
+#include "NVDataMgmt.h"
 #include "OperationModes.h"
+#include "PresOccl.h"
+#include "RTC.h"
 #include "SafetyShutdown.h"
 #include "SystemComm.h"
 #include "TaskBG.h"
 #include "Timers.h"
+#include "TreatmentStop.h"
 #include "WatchdogMgmt.h"
 
 static void initProcessor( void );
@@ -123,8 +133,18 @@
 static void initProcessor( void )
 {
     gioInit();      // configure GPIO pins
+    adcInit();      // configure internal ADC channels
     mibspiInit();   // re-purposing MIBSPI5 I/O/C pins as GPIO
+    etpwmInit();    // configure PWMs
+        etpwmSetCmpA( etpwmREG1, 0 );
+        etpwmSetCmpA( etpwmREG2, 0 );
+        etpwmSetCmpA( etpwmREG3, 0 );
+        etpwmSetCmpA( etpwmREG4, 0 );
+        etpwmSetCmpA( etpwmREG6, 0 );
+        etpwmSetCmpA( etpwmREG7, 0 );
+        etpwmStartTBCLK();
     canInit();      // CAN1 = CAN, re-purposing CAN2 and CAN3 Rx and Tx pins as GPIO
+        //canEnableloopback( canREG1, External_Lbk );  // TODO - debug code
     sciInit();      // SCI1 used for PC serial interface, SCI2 used for FPGA serial interface
     dmaEnable();    // enable DMA
 }
@@ -139,17 +159,26 @@
  *************************************************************************/
 static void initSoftware( void )
 {
+    initAlarmMgmt();
     initTimers();
-    initSafetyShutdown();
     initCPLD();
-    initAlarmLamp();
-    initButtons();
+    initSafetyShutdown();
     initWatchdogMgmt();
     initFPGA();
+    initAlarmLamp();
+    initButtons();
+    initInternalADC();
     initCommBuffers();
     initMsgQueues();
     initSystemComm();
+    initPresOccl();
+    initBloodFlow();
+    initDialInFlow();
+    initDialysis();
+    initTreatmentStop();
     initOperationModes();
+    initRTC();
+    initNVDataMgmt();
 }
 
 /*************************************************************************