Advice on upgrading Servers from win Server 2003 to 2008 r2

Hello all, I have a few questions , the small business I work for , is in desperate need to update there servers. All the machines are running Windows Server 2003 SP2 Standard Edition. 

1. Server 1 - Intel Xeon 3.00Ghz 4GB RAM  - Runs Microsoft SQL Server -  No Server Roles 
2. Server 2 - Intell Xeon 3.00Ghz 4GB RAM - Runs Our CMS (Successware21) - Server Roles: File Server, Print Server, DomainController, DNS Server, DHCP Server, WINS.
3. Server 3 - intell Xeon 5310 1.6Ghz  2.00 GB RAM - Runs Microsoft SQL Server - Server Roles: File Server, Application Server, Terminal Server, Remote Access/VPN 
4. ABOUT 100 Desktops running Windows 7, only need about 5 Remote Desktop Users ,  

I have never had to buy CALS ,and it can get quite confusing, want to see if I have this figured out right, or if Im missing something.

So here is what I have so far . . 

What Software I think I need:

1. Server 1 - 1 Windows Server 2008 R2 Standard (comes with 5CALS((not sure if these are User or Device))) , 1 copy of SQL Server 2008 R2.
2. Server 2 - 1 Windows Server 2008 R2 Standard  (comes with 5 CALS((not sure if these are User or Device))) ,Successware21 is licensed per processor(so I dont think Ill need any more CALS for This)) 
3. server 3 -  1 Windows Server 2008 R2 Standard (comes with 5 CALS((not sure if these are User or Device))) , 1 copy of SQL Server 2008 R2.
4. Desktops - (not including the 5 CALS that come with the server software) 80 Device CALS(many users will be using same machine turnover on employees is quite high), 5 RDS CALS ( for ppl who ned remote access). 

Questions: 

1. What kind of CALS some with the Server 2008 R2 , User or Device?
2. SQL users, as far as i can tell there are only 2 user logins(including 'sa' user),no person other than myself use and Successware21 use the database, do i need any additional licensing or CALS?
3. I have several Linux machines running centos that pull some queries from the Microsoft SQL Server, for reports, are any addt'l CALS required for these machines, or can I simply use the 'sa' login?

Please any advice would be grand, this is quite a large upgrade, and I have never done anything to this magnitude any experience /advice is greatly appreciated.