some upgrade question and 404 error

[lordi]

hello, I have IP.Board 3.4.9 and make a test upgrade from it

make dev folder inside root and copy all script there and duplicate database.

re-setting global-conf, and try to upgrade to 4.1.17

I have some question :

1. Is it okay if we keep all plugin and custom themes active while we do upgrade or better disable all 3rd party plugin and custom themes back to default IPB themes?

2. I have relatively low activity forum so I use manual background processing using browser,  so when this manual activity run, do we need to keep the browser active, or we can safely close it, and the manual processing still running?

3. I have cron capability on my shared hosting, how exactly I have to do to run this cron job for this upgrade, is it okay when I just pick the cron job as an my option save it and then add the cron script to my cron job queue? how do we know when the cron is finish? 

3. I notice when using manual processing, I got error on browser (I dont remember the notification, but related in display page error) but when I refreshed the browser the process running again, is it okay?

4. After manual processing , I got notification upgrade succeeded and then login to admin, I try all category and sub forum but all display 404 error, basically only home and admin pages that work, and I saw in admin panel under seo pages something bout failures in rewriting and then I came up with .htaccess editing

I add /dev on RewriteEngine and RewriteRule

AddType application/x-httpd-php56 php

php_value suhosin.get.max_vars 5000

<IfModule mod_rewrite.c>
Options -MultiViews
RewriteEngine On
RewriteBase /dev
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule \.(jpeg|jpg|gif|png)$ /public/404.php [NC,L]

RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /dev/index.php [L]
</IfModule>

after that, all seems fine.

is it a correct fix? or I still miss something?

sorry for so much newbie question, after this dev upgrade, my plan is to upgrade my live sites, little bit nervous bout that