From theory, the 1.3 shouldn't have any influence on your framerate over the 1.2 release. There aren't any changes included which would lead to a negative performance impact.
I think that Mark pointed in the very right direction, saying

Quote:

I do get better frame rates with the VC-137 and E-3. I assume that it is because they don't have the passenger cabin or cargo deck, only the VC.

So please make sure to have the (passenger) cabin disabled in the ACE tool (you have to reset this setting after installing 1.3) when running the plane on a slower system.

Concerning the framelimiter, I think there's a readme included but in case you still struggle there, here are some threads which might help you. It's mainly a thing of pointing the limiter to the FSX.exe and also setting up the desired framerate then.
http://forum.avsim.net/topic/329315-how-do-you-install-fps-limiter-in-win7/page__p__1946669__hl__fps+limiter__fromsearch__1#entry1946669

http://forum.avsim.net/topic/329524-fps-limiter-v02/page__p__1945171__hl__fps+limiter__fromsearch__1#entry1945171