diff --git a/klippy/gcode.py b/klippy/gcode.py
index 2c57ed49..e4798159 100644
--- a/klippy/gcode.py
+++ b/klippy/gcode.py
@@ -59,7 +59,6 @@ class GCodeParser:
                                    for h in handlers)
     def run(self):
         self.fd_handle = self.reactor.register_fd(self.fd, self.process_data)
-        self.reactor.run()
     def finish(self):
         self.reactor.end()
         self.toolhead.motor_off()
diff --git a/klippy/klippy.py b/klippy/klippy.py
index 191997c5..ed71d699 100644
--- a/klippy/klippy.py
+++ b/klippy/klippy.py
@@ -45,8 +45,11 @@ class Printer:
 
         self.gcode = gcode.GCodeParser(
             self, pseudo_tty, inputfile=debuginput is not None)
-        self.mcu = None
-        self.stat_timer = None
+        self.mcu = mcu.MCU(self, ConfigWrapper(self, 'mcu'))
+        self.stats_timer = self.reactor.register_timer(
+            self.stats, self.reactor.NOW)
+        self.connect_timer = self.reactor.register_timer(
+            self.connect, self.reactor.NOW)
 
         self.objects = {}
         if self.fileconfig.has_section('fan'):
@@ -73,18 +76,20 @@ class Printer:
             self.objects[oname].build_config()
         self.gcode.build_config()
         self.mcu.build_config()
-    def connect(self):
-        self.mcu = mcu.MCU(self, ConfigWrapper(self, 'mcu'))
+    def connect(self, eventtime):
         self.mcu.connect()
         self.build_config()
-        self.stats_timer = self.reactor.register_timer(
-            self.stats, self.reactor.NOW)
+        self.gcode.run()
+        self.reactor.unregister_timer(self.connect_timer)
+        return self.reactor.NEVER
     def connect_file(self, output, dictionary):
-        self.mcu = mcu.MCU(self, ConfigWrapper(self, 'mcu'))
+        self.reactor.update_timer(self.stats_timer, self.reactor.NEVER)
         self.mcu.connect_file(output, dictionary)
         self.build_config()
-    def run(self):
         self.gcode.run()
+        self.reactor.unregister_timer(self.connect_timer)
+    def run(self):
+        self.reactor.run()
         # If gcode exits, then exit the MCU
         self.stats(time.time())
         self.mcu.disconnect()
@@ -141,8 +146,6 @@ def main():
     if debugoutput:
         proto_dict = read_dictionary(options.read_dictionary)
         printer.connect_file(debugoutput, proto_dict)
-    else:
-        printer.connect()
     printer.run()
 
     if bglogger is not None:
diff --git a/klippy/mcu.py b/klippy/mcu.py
index ba95d92c..d279a847 100644
--- a/klippy/mcu.py
+++ b/klippy/mcu.py
@@ -342,12 +342,13 @@ class MCU:
         self._steppersync = self.ffi_lib.steppersync_alloc(
             self.serial.serialqueue, stepqueues, len(stepqueues), count)
     def connect(self):
+        state_params = {}
         def handle_serial_state(params):
-            if params['#state'] == 'connected':
-                self._printer.reactor.end()
+            state_params.update(params)
         self.serial.register_callback(handle_serial_state, '#state')
         self.serial.connect()
-        self._printer.reactor.run()
+        while state_params.get('#state') != 'connected':
+            self._printer.reactor.pause(time.time() + 0.05)
         self.serial.unregister_callback('#state')
         logging.info("serial connected")
         self._mcu_freq = float(self.serial.msgparser.config['CLOCK_FREQ'])
@@ -427,14 +428,15 @@ class MCU:
         sent_config = False
         def handle_get_config(params):
             config_params.update(params)
-            done = not sent_config or params['is_config']
-            if done:
-                self._printer.reactor.end()
-            return done
+            return True
         while 1:
             self.serial.send_with_response(msg, handle_get_config, 'config')
-            self._printer.reactor.run()
-            if not config_params['is_config']:
+            while 1:
+                is_config = config_params.get('is_config')
+                if is_config is not None and (not sent_config or is_config):
+                    break
+                self._printer.reactor.pause(time.time() + 0.05)
+            if not is_config:
                 # Send config commands
                 for c in self._config_cmds:
                     self.send(self.create_command(c))
diff --git a/klippy/serialhdl.py b/klippy/serialhdl.py
index 619d46ce..a52a8130 100644
--- a/klippy/serialhdl.py
+++ b/klippy/serialhdl.py
@@ -59,7 +59,7 @@ class SerialReader:
     def connect(self):
         logging.info("Starting serial connect")
         self.ser = serial.Serial(self.serialport, self.baud, timeout=0)
-        stk500v2_leave(self.ser)
+        stk500v2_leave(self.ser, self.reactor)
         self.serialqueue = self.ffi_lib.serialqueue_alloc(self.ser.fileno(), 0)
         SerialBootStrap(self)
         self.background_thread = threading.Thread(target=self._bg_thread)
@@ -269,7 +269,7 @@ class SerialBootStrap:
             params['#msgid'], len(params['#msg'])))
 
 # Attempt to place an AVR stk500v2 style programmer into normal mode
-def stk500v2_leave(ser):
+def stk500v2_leave(ser, reactor):
     logging.debug("Starting stk500v2 leave programmer sequence")
     origbaud = ser.baudrate
     # Request a dummy speed first as this seems to help reset the port
@@ -277,10 +277,10 @@ def stk500v2_leave(ser):
     ser.read(1)
     # Send stk500v2 leave programmer sequence
     ser.baudrate = 115200
-    time.sleep(0.100)
+    reactor.pause(time.time() + 0.100)
     ser.read(4096)
     ser.write('\x1b\x01\x00\x01\x0e\x11\x04')
-    time.sleep(0.050)
+    reactor.pause(time.time() + 0.050)
     res = ser.read(4096)
     logging.debug("Got %s from stk500v2" % (repr(res),))
     ser.baudrate = origbaud