Please provide a list of installed plugins and their versions, as well as a sample config.xml of such a 'large job'.

The list of the installed plugins (copied from display of the system properties):

ant 1.2 true true
antisamy-markup-formatter 1.3 true true
any-buildstep 0.1 true false
artifactdeployer 0.33 true false
audit-trail 2.1 true false
backup 1.6.1 true false
batch-task 1.17 true false
build-blocker-plugin 1.6 true false
build-environment 1.4 true false
build-pipeline-plugin 1.4.7 true false
build-user-vars-plugin 1.4 true false
clone-workspace-scm 0.6 true false
conditional-buildstep 1.3.3 true false
config-file-provider 2.7.5 true false
copy-to-slave 1.4.4 true false
copyartifact 1.35 true false
credentials 1.22 true true
custom-tools-plugin 0.4.4 true false
CustomHistory 1.6 true false
cvs 2.12 true true
dashboard-view 2.9.4 true false
delivery-pipeline-plugin 0.8.11 true false
dependencyanalyzer 0.7 true false
deploy 1.10 true false
disk-usage 0.25 true false
downstream-buildview 1.9 true false
downstream-ext 1.8 true false
dynamic-axis 1.0.3 true false
dynamic_extended_choice_parameter 1.0.1 true false
dynamicparameter 0.2.0 true false
email-ext 2.39.3 true false
envfile 1.2 true false
envinject 1.91.2 true false
extended-choice-parameter 0.35 true false
extensible-choice-parameter 1.2.2 true false
external-monitor-job 1.4 true true
flexible-publish 0.15.1 true false
git 2.3.5 true false
git-client 1.16.1 true false
git-server 1.6 true false
groovy 1.24 true false
groovy-label-assignment 1.1.0 true false
groovyaxis 0.3 true false
ivy 1.24 true false
javadoc 1.3 true true
job-log-logger-plugin 1.0 true false
job-node-stalker 1.0.3 true false
jobConfigHistory 2.10 true false
jquery 1.11.2-0 true false
jquery-ui 1.0.2 true false
junit 1.5 true true
labeled-test-groups-publisher 1.2.7 true false
ldap 1.11 true true
m2-repo-reaper 1.0 true false
mailcommander 1.0.0 true false
mailer 1.15 true true
managed-scripts 1.1.1 true false
mantis 0.26 true false
mapdb-api 1.0.6.0 true false
matrix-auth 1.2 true true
matrix-combinations-parameter 1.0.7 true false
matrix-project 1.4.1 true false
Matrix-sorter-plugin 1.1 true false
maven-plugin 2.9 true true
metadata 1.1.0b true false
metrics 3.0.9 true false
monitoring 1.55.0 true false
nodelabelparameter 1.5.1 true false
pam-auth 1.2 true true
parameterized-trigger 2.26 true false
periodicbackup 1.3 true false
postbuild-task 1.8 true false
postbuildscript 0.17 true false
PrioritySorter 2.11 true false
role-strategy 2.2.0 true false
run-condition 1.0 true false
scm-api 0.2 true false
script-security 1.13 true false
scriptler 2.7 true false
selection-tasks-plugin 1.0 true false
shared-objects 0.44 true false
show-build-parameters 1.0 true false
skip-certificate-check 1.0 true false
sonar 2.2 true false
ssh-credentials 1.11 true true
ssh-slaves 1.9 true true
statusmonitor 1.3 true false
strawboss 1.3 true false
subversion 2.5 true true
support-core 2.20 true false
svn-tag 1.17 true false
testlink 3.10 true false
throttle-concurrents 1.8.4 true false
token-macro 1.10 true false
translation 1.12 true true
uno-choice 0.24 true false
update-sites-manager 1.0.1 true false
validating-string-parameter 2.3 true false
vsphere-cloud 2.4 true false
weblogic-deployer-plugin 3.2 true false
websphere-deployer 1.3-SNAPSHOT (private-08/05/2014 09:34-nothhard) true false
windows-slaves 1.0 true false
ws-cleanup 0.25 true false
xunit 1.94 true false

The attached zip file contains the config.xml file from a job called DOXiS4_CSB-Test-All-Comb".
Opening this job for configuration exceeds the limit of 100 seconds configured in my firefox-browser.
During this time one core of the quad-core-cpu is busy for the whole time.

I increased the timeout value for scripts to run to 200 seconds.
The start to configure the job I added in the attachments took 180 seconds (yes 3 minutes) on my machine.

If I should present the data in a special way or format, please feel free to contact me.

Haven't had time to investigate, but you could do some of that yourself:
While the form is submitted and the page is loading, repeatedly load the /threadDump URL and look for a thread named Handling POST /job/JOBNAME/configSubmit or something similar. Look where it's stuck processing for most of the time.

Excuse my late answer.
I am glad that I can help.
I started configuring the job I added in this call as example.
The browser was about 3 minutes in the state loading data.
At this time a call to the threadDump URL does not show a thread "Handling POST" or "configSubmit".
The only Thread with Hanling was the threadDump itself.

It look like jenkins generates Javascript, which runs all the time in the browser.
It seems it runs a lot longer, if there a more objects or lines to display.

Skript: http://sst-bld-master.sst.loca…/0da8a904/scripts/prototype.js:2188

It seems the script is calculating the size of the objects to display.