500 Server Error after deployment
Did you have "Clean URLs" enabled on the Windows install?  You may need mod_rewrite enabled in Apache (a2enmod rewrite)

I'm not sure how your server is configured (os/php version/etc), but I had a similar issue that required me to change the following in .htaccess

# RewriteBase /
to 
RewriteBase /


Another thing to check would be that overrides are allowed at all.  Apache needs to be set to something like "AllowOverride All"

More info regarding AllowOverride:

How can I enable clean URLs?

How to enable Clean URLs?

Regarding permissions, there is a bunch of information available including a script that can help repair permissions (obviously use extreme caution when running and verify before you do.) 

Source for the script below.

#!/bin/bash

# Help menu
print_help() {
cat &lt;&lt;-HELP
This script is used to fix permissions of a Drupal installation
you need to provide the following arguments:

  1) Path to your Drupal installation.
  2) Username of the user that you want to give files/directories ownership.
  3) HTTPD group name (defaults to www-data for Apache).

Usage: (sudo) bash ${0##*/} --drupal_path=PATH --drupal_user=USER --httpd_group=GROUP
Example: (sudo) bash ${0##*/} --drupal_path=/usr/local/apache2/htdocs --drupal_user=john --httpd_group=www-data
HELP
exit 0
}

if [ $(id -u) != 0 ]; then
  printf "**************************************\n"
  printf "* Error: You must run this with sudo or root*\n"
  printf "**************************************\n"
  print_help
  exit 1
fi

drupal_path=${1%/}
drupal_user=${2}
httpd_group="${3:-www-data}"

# Parse Command Line Arguments
while [ "$#" -gt 0 ]; do
  case "$1" in
    --drupal_path=*)
        drupal_path="${1#*=}"
        ;;
    --drupal_user=*)
        drupal_user="${1#*=}"
        ;;
    --httpd_group=*)
        httpd_group="${1#*=}"
        ;;
    --help) print_help;;
    *)
      printf "***********************************************************\n"
      printf "* Error: Invalid argument, run --help for valid arguments. *\n"
      printf "***********************************************************\n"
      exit 1
  esac
  shift
done

if [ -z "${drupal_path}" ] || [ ! -d "${drupal_path}/sites" ] || [ ! -f "${drupal_path}/core/modules/system/system.module" ] &amp;&amp; [ ! -f "${drupal_path}/modules/system/system.module" ]; then
  printf "*********************************************\n"
  printf "* Error: Please provide a valid Drupal path. *\n"
  printf "*********************************************\n"
  print_help
  exit 1
fi

if [ -z "${drupal_user}" ] || [[ $(id -un "${drupal_user}" 2&gt; /dev/null) != "${drupal_user}" ]]; then
  printf "*************************************\n"
  printf "* Error: Please provide a valid user. *\n"
  printf "*************************************\n"
  print_help
  exit 1
fi

cd $drupal_path
printf "Changing ownership of all contents of "${drupal_path}":\n user =&gt; "${drupal_user}" \t group =&gt; "${httpd_group}"\n"
chown -R ${drupal_user}:${httpd_group} .

printf "Changing permissions of all directories inside "${drupal_path}" to "rwxr-x---"...\n"
find . -type d -exec chmod u=rwx,g=rx,o= '{}' \;

printf "Changing permissions of all files inside "${drupal_path}" to "rw-r-----"...\n"
find . -type f -exec chmod u=rw,g=r,o= '{}' \;

printf "Changing permissions of "files" directories in "${drupal_path}/sites" to "rwxrwx---"...\n"
cd sites
find . -type d -name files -exec chmod ug=rwx,o= '{}' \;

printf "Changing permissions of all files inside all "files" directories in "${drupal_path}/sites" to "rw-rw----"...\n"
printf "Changing permissions of all directories inside all "files" directories in "${drupal_path}/sites" to "rwxrwx---"...\n"
for x in ./*/files; do
  find ${x} -type d -exec chmod ug=rwx,o= '{}' \;
  find ${x} -type f -exec chmod ug=rw,o= '{}' \;
done
echo "Done setting proper permissions on files and directories"