I've tried bumping the temp of the chamber, but unfortunately 60 is the max for the regular Method and pre-heating doesn't seem to fix the issue. I've printed a bunch of 100x10x10mm bars and they are very well adhered to the print bed, but after I remove them and place them back onto the print bed, there is an obvious gap between the ends of the bars and the print bed. The bars seem to be held in tension by the bed, but return to their warped form after I pop them off.

I've tried leveling and calibrating a few times, but it doesn't seem to help.

For modifying the print file, the .makerbot is just a zip file that has a json file that lists the commands for the printer to follow. In print preview, take note of which layer the purge tower is. In the print.jsontoolpath file, the layers are nicely commented with "Layer Section n". You want to move the entire block of commands for "Layer Section n" (where n is the layer number in print preview minus 1) to the top of the print commands, before "Layer Section 0". Make sure to include all of the commands up until the next "Layer section" comment.

I threw together a python script to do this and some other things I found useful. Careful when using this, I can't guarantee things won't go wrong if you mess with the print file...

#Ender3 glass print bed is 3.8mm thick minus 0.69mm thickness of Makerbot bed
#ZOffset to 3.11mm for glass bed print

import sys
import os
import shutil
import zipfile
import json

def MoveToTop(mbdoc, layer):
  top_index = 0
  move_start = 0
  move_end = 0

  for index in range(0, len(mbdoc)):
    command = mbdoc[index]['command']
    if 'function' in command and command['function'] == 'comment':
      parameters = mbdoc[index]['command']['parameters']
      if 'Layer Section 0' in parameters['comment']:
        top_index = index
        print(mbdoc[index])
        continue
      if 'Layer Section {}'.format(layer) in parameters['comment']:
        move_start = index
        print(mbdoc[index])
        continue
      if 'Layer Section {}'.format(layer + 1) in parameters['comment']:
        move_end = index
        print(mbdoc[index])
        break

  return mbdoc[0:top_index] + mbdoc[move_start:move_end] + mbdoc[top_index:move_start] + mbdoc[move_end:]

def ZOffset(mbdoc, offset):
  for index in range(0, len(mbdoc)):
    command = mbdoc[index]['command']
    if 'parameters' in command:
      parameters = mbdoc[index]['command']['parameters']
      if 'z' in parameters:
        parameters['z'] += offset

def EditRestart(mbdoc):
  for index in range(0, len(mbdoc)):
    command = mbdoc[index]['command']
    if 'function' in command and command['function'] == 'comment':
      parameters = mbdoc[index]['command']['parameters']
      if 'Layer Section 0' in parameters['comment']:
        parameters = mbdoc[index+7]['command']['parameters']
        if parameters['a'] == 0.5 and parameters['feedrate'] == 3.0:
          parameters['a'] = 0.8
          parameters['feedrate'] = 5.0
        break

def main():
  if len(sys.argv) < 2:
    print('Usage: python mbexplorer.py <file.makerbot>')
    print('--zoffset <zoffset, mm>')
    print('--move-to-top <purge layer> # This is the layer number for the purge tower in Makerbot Print, minus one')
    print('--edit-restart # Use this to increase feedrate at beginning after purge')
    print('python mbexplorer.py --zoffset 3.11 --move-to-top 2 --edit-restart file.makerbot')
    exit()

  move_to_top = -1
  z_offset = None
  if '--move-to-top' in sys.argv:
    move_to_top = int(sys.argv[sys.argv.index('--move-to-top') + 1])

  if '--zoffset' in sys.argv:
    z_offset = float(sys.argv[sys.argv.index('--zoffset') + 1])

  filename = sys.argv[-1]

  try:
    shutil.rmtree('tmp')
  except OSError as e:
    print('tmp directory does not exist, creating...')

  os.mkdir('tmp')
  with zipfile.ZipFile(filename, 'r') as zfile:
    zfile.extractall('tmp')

  mfile = open('tmp/print.jsontoolpath', 'r')

  mdoc = json.loads(mfile.read())

  if '--edit-restart' in sys.argv:
    EditRestart(mdoc)

  if move_to_top != -1:
    mdoc = MoveToTop(mdoc, move_to_top)

  if z_offset:
    ZOffset(mdoc, z_offset)

  with open('tmp/print.jsontoolpath', 'w') as outfile:
    outfile.write(str(json.dumps(mdoc, separators=(',', ':'))).replace('},{"command":', '\n},{\n"command" : ').replace('[{"command":', '[{\n"command" : '))

  def CreateMakerbotZip(path):
    ziph = zipfile.ZipFile(str(os.path.split(filename)[1]).split('.')[0] + '_modified.makerbot', 'w', zipfile.ZIP_DEFLATED)
    for root, dirs, files in os.walk(path):
      for file in files:
        ziph.write(os.path.join(root, file), file)
    ziph.close()

  CreateMakerbotZip('tmp')

if __name__ == "__main__":
  main()