A NiFi template for the ExecuteScript processor that uses Jython to convert string timestamps to longs in JSON. Based on @mattyb149's template (https://gist.github.com/mattyb149/89205fcbc6d0e15ba024)

gistfile1.txt

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<template>
  <description>Converts string timestamps to long in JSON.
  </description>
  <name>ConvertStringTimestampsToLong</name>
  <snippet>
    <processors>
      <id>c6cf8df9-bfcf-45e9-ab06-76de85e78f78</id>
      <parentGroupId>a27e19b1-ef3e-41a2-b0ce-266370b14b47</parentGroupId>
      <position>
        <x>1233.620849609375</x>
        <y>5.457275390625</y>
      </position>
      <config>
        <bulletinLevel>WARN</bulletinLevel>
        <comments></comments>
        <concurrentlySchedulableTaskCount>1</concurrentlySchedulableTaskCount>
        <defaultConcurrentTasks>
          <entry>
            <key>TIMER_DRIVEN</key>
            <value>1</value>
          </entry>
          <entry>
            <key>EVENT_DRIVEN</key>
            <value>0</value>
          </entry>
          <entry>
            <key>CRON_DRIVEN</key>
            <value>1</value>
          </entry>
        </defaultConcurrentTasks>
        <defaultSchedulingPeriod>
          <entry>
            <key>TIMER_DRIVEN</key>
            <value>0 sec</value>
          </entry>
          <entry>
            <key>CRON_DRIVEN</key>
            <value>* * * * * ?</value>
          </entry>
        </defaultSchedulingPeriod>
        <descriptors>
          <entry>
            <key>Script Engine</key>
            <value>
              <allowableValues>
                <displayName>ECMAScript</displayName>
                <value>ECMAScript</value>
              </allowableValues>
              <allowableValues>
                <displayName>Groovy</displayName>
                <value>Groovy</value>
              </allowableValues>
              <allowableValues>
                <displayName>lua</displayName>
                <value>lua</value>
              </allowableValues>
              <allowableValues>
                <displayName>python</displayName>
                <value>python</value>
              </allowableValues>
              <allowableValues>
                <displayName>ruby</displayName>
                <value>ruby</value>
              </allowableValues>
              <defaultValue>ECMAScript</defaultValue>
              <description>The engine to execute scripts</description>
              <displayName>Script Engine</displayName>
              <dynamic>false</dynamic>
              <name>Script Engine</name>
              <required>true</required>
              <sensitive>false</sensitive>
              <supportsEl>false</supportsEl>
            </value>
          </entry>
          <entry>
            <key>Script File</key>
            <value>
              <description>Path to script file to execute. Only one of Script File or Script Body may be used
              </description>
              <displayName>Script File</displayName>
              <dynamic>false</dynamic>
              <name>Script File</name>
              <required>false</required>
              <sensitive>false</sensitive>
              <supportsEl>true</supportsEl>
            </value>
          </entry>
          <entry>
            <key>Script Body</key>
            <value>
              <description>Body of script to execute. Only one of Script File or Script Body may be used</description>
              <displayName>Script Body</displayName>
              <dynamic>false</dynamic>
              <name>Script Body</name>
              <required>false</required>
              <sensitive>false</sensitive>
              <supportsEl>false</supportsEl>
            </value>
          </entry>
          <entry>
            <key>Module Directory</key>
            <value>
              <description>Comma-separated list of paths to files and/or directories which contain modules required by
                the script.
              </description>
              <displayName>Module Directory</displayName>
              <dynamic>false</dynamic>
              <name>Module Directory</name>
              <required>false</required>
              <sensitive>false</sensitive>
              <supportsEl>false</supportsEl>
            </value>
          </entry>
          <entry>
            <key>endTime</key>
            <value>
              <description></description>
              <displayName>endTime</displayName>
              <dynamic>true</dynamic>
              <name>endTime</name>
              <required>false</required>
              <sensitive>false</sensitive>
              <supportsEl>true</supportsEl>
            </value>
          </entry>
          <entry>
            <key>mrt</key>
            <value>
              <description></description>
              <displayName>mrt</displayName>
              <dynamic>true</dynamic>
              <name>mrt</name>
              <required>false</required>
              <sensitive>false</sensitive>
              <supportsEl>true</supportsEl>
            </value>
          </entry>
          <entry>
            <key>rt</key>
            <value>
              <description></description>
              <displayName>rt</displayName>
              <dynamic>true</dynamic>
              <name>rt</name>
              <required>false</required>
              <sensitive>false</sensitive>
              <supportsEl>true</supportsEl>
            </value>
          </entry>
          <entry>
            <key>startTime</key>
            <value>
              <description></description>
              <displayName>startTime</displayName>
              <dynamic>true</dynamic>
              <name>startTime</name>
              <required>false</required>
              <sensitive>false</sensitive>
              <supportsEl>true</supportsEl>
            </value>
          </entry>
        </descriptors>
        <lossTolerant>false</lossTolerant>
        <penaltyDuration>30 sec</penaltyDuration>
        <properties>
          <entry>
            <key>Script Engine</key>
            <value>python</value>
          </entry>
          <entry>
            <key>Script File</key>
          </entry>
          <entry>
            <key>Script Body</key>
            <value>
import json
import java.io
import time
import datetime
from org.apache.commons.io import IOUtils
from java.nio.charset import StandardCharsets
from org.apache.nifi.processor.io import StreamCallback

class PyStreamCallback(StreamCallback):
  def __init__(self, properties):
    self.properties = properties

  def process(self, inputStream, outputStream):
    text = IOUtils.toString(inputStream, StandardCharsets.UTF_8)
    obj = json.loads(text)

    for key in self.properties:
      if key.isDynamic() and key.getName() in obj:
        obj[key.getName()] = int(time.mktime(datetime.datetime.strptime(obj[key.getName()], self.properties[key]).timetuple()) * 1000)

    outputStream.write(bytearray(json.dumps(obj, indent=4).encode('utf-8')))

flowFile = session.get()                                  
properties = context.getProperties()
if (flowFile != None):                                     
  flowFile = session.write(flowFile,PyStreamCallback(properties))
  flowFile = session.putAttribute(flowFile, &quot;filename&quot;, flowFile.getAttribute('filename').split('.')[0]+'_translated.json')
  session.transfer(flowFile, REL_SUCCESS)
            </value>
          </entry>
          <entry>
            <key>Module Directory</key>
          </entry>
          <entry>
            <key>endTime</key>
            <value>%Y-%m-%d %H:%M:%S.%f</value>
          </entry>
          <entry>
            <key>mrt</key>
            <value>%Y-%m-%d %H:%M:%S.%f</value>
          </entry>
          <entry>
            <key>rt</key>
            <value>%Y-%m-%d %H:%M:%S.%f</value>
          </entry>
          <entry>
            <key>startTime</key>
            <value>%Y-%m-%d %H:%M:%S.%f</value>
          </entry>
        </properties>
        <runDurationMillis>0</runDurationMillis>
        <schedulingPeriod>0 sec</schedulingPeriod>
        <schedulingStrategy>TIMER_DRIVEN</schedulingStrategy>
        <yieldDuration>1 sec</yieldDuration>
      </config>
      <name>ExecuteScriptConvertTimestampsToLongs</name>
      <relationships>
        <autoTerminate>true</autoTerminate>
        <description>FlowFiles that failed to be processed</description>
        <name>failure</name>
      </relationships>
      <relationships>
        <autoTerminate>false</autoTerminate>
        <description>FlowFiles that were successfully processed</description>
        <name>success</name>
      </relationships>
      <state>RUNNING</state>
      <style/>
      <supportsEventDriven>false</supportsEventDriven>
      <supportsParallelProcessing>false</supportsParallelProcessing>
      <type>org.apache.nifi.processors.script.ExecuteScript</type>
    </processors>
  </snippet>
  <timestamp>05/26/2016 12:18:00 EDT</timestamp>
</template>

Example configuration. The property name is the name of the JSON field to convert and the value is the (Python) timestamp format.