R – .htaccess redirect www.domain.com to sub.domain.com but only for root

You can use a rewrite rule that uses ^$ to represent the root and rewrite that to your /store directory, like this:

RewriteEngine On
RewriteRule ^$ /store [L]

To first force HTTPS, you must check the correct environment variable %{HTTPS} off, but your rule above then prepends the www. Since you have a second rule to enforce www., don't use it in the first rule.

RewriteEngine On
RewriteCond %{HTTPS} off
# First rewrite to HTTPS:
# Don't put www. here. If it is already there it will be included, if not
# the subsequent rule will catch it.
RewriteRule .* https://%{HTTP_HOST}%{REQUEST_URI} [L,R=301]
# Now, rewrite any request to the wrong domain to use www.
# [NC] is a case-insensitive match
RewriteCond %{HTTP_HOST} !^www\. [NC]
RewriteRule .* https://www.%{HTTP_HOST}%{REQUEST_URI} [L,R=301]

About proxying

When behind some forms of proxying, whereby the client is connecting via HTTPS to a proxy, load balancer, Passenger application, etc., the %{HTTPS} variable may never be on and cause a rewrite loop. This is because your application is actually receiving plain HTTP traffic even though the client and the proxy/load balancer are using HTTPS. In these cases, check the X-Forwarded-Proto header instead of the %{HTTPS} variable. This answer shows the appropriate process