If the issue really is that there is just a ton of stuff going back and forth
This is the frustrating thing about AC and SQL. Obviously, AC has to use the free version of SQL Express 2005 and 2012. They can't expect for all their users to keep paying for the full or standard versions of SQL. So Express is bundled in the install. The problem is that comes with a big hit. While 2012 gives you 10 GB of space, quite a bit more than 2005, they are all crippled with the same 1 GB of memory. Standard versions come with a ton of RAM or unlimited RAM. So, when you put 40 GBs of RAM in your server, you are wasting quite a bit of RAM. SQL will take as much RAM as you give it, so in this case, you would set it to 24 or so. Maybe even 30 GBs. Now you have enough RAM to store 24 times the amount of pages or each query. This is based on the fact that statistically, you will be using the same patients more frequently for a certain length of time just like you will see Patient A five times in two weeks, and then not see him or her for two months. So, the patient query you used two weeks ago is stored as RAM in SQL. So, just like RAM on a computer, the queries you use within RAM, are going to be much faster than the queries that go to the AC folder and the AmazingCharts.mdf database. This is where a server can be more efficient than a regular OS. It goes months without a reboot. Every time you reboot, the cache is cleared. So, in this instance, pardon the pun, not rebooting is more productive. The reason a lot of users state they have better performance when they reboot is because they have 4 GBs of RAM to run AC, their billing software, all their services, background programs, etc. This is really 3.2 GBs. So when SQL takes 1 GB of RAM, now the available RAM is 2.2 GBs of RAM. That just isn't enough to go around. So a reboot puts all the RAM back in play. Which is why a 64-bit OS is so helpful. You can add a lot of RAM. It's cheap.
One thing that may help is SQL 2012 Standard. But, you would need to have it installed by an expert, even remotely. But, I would make sure that is an issue. Of course it can't hurt.