Modules contains ports. Modules are inserted into slots just like PCI slots.Yes the LAG primary port is always port 29 .Primary ports are nothing but normal ethernet port on WLC which plugs into the switch.
Here is a description of the ports on the 4404 WLC licensed for 100 AP support:
--"AIR-WLC4404-100-K9?This 4404-100 controller uses four GigE connections to bypass one or two single network failures, and communicates with up to 100 access points. It has two back-panel slots for future expansion modules."--
When connecting more than 50 AP's, you have to configure additional AP Manager interfaces on the configuration page and in order to connect all 4 SFP interfaces you will need 3 additional AP Manager interfaces i.e - 4 AP Manager interfaces = 1 per physical port.