1&2) This depends on which type of authentication you are using for SQL server. If NT, then your Dispatcher, MDS, Policy, and Sync services need to use the NT account which has access to the SQL db. If you are using SQL authentication, i.e. a SQL username and password vs. NT, then the account the services run under (i.e. the account the BES is installed under) should just be an admin of the server itself.
For the nitty gritty on SQL permissions required for BES Domino check out this series of blog posts: BlackBerry Enterprise Server on Domino Discussion: BES SQL Permissions Explained - Part 0
3) Notes & Domino use port 1352 to communicate internally. BES does not use this outbound to connect with the NOC, just 3101 like Exchange.
4) Make sure to create your BlackBerryAdmins group which contains your notes BB admins and also the LocalDomainServers group. The LocalDomainServers group also must contain your BES servers, which is how they access the BB user's mailfiles and state databases. It is normal to put all Domino servers into this special group so your Domino admins should understand.
5) Don't see why not... you can RDP to the console of the servers by using the "connect to console:i:1" line in the .rdp file. This is very useful in a Domino environment b/c the Domino console only appears on the console, not under any other user terminal session. And sometimes you need to interact with the console directly.