No worries Mike, this would be like me stumbling around trying to get an old welder to stick two pieces of metal together. The instruction kinda suck and seem geared toward getting a serial (DB9) controller to work.
Cat 5 or Cat 6 will not matter for this type of application. Cat 6 is just the newest rating higher speeds. If you made your own cable, it is very easy to cross wires. Check the communication and LED sequencing with a known good cable, I believe you should get flashing LEDs even if your setup isn't 100% correct. You have to have the LED flashing to have communication.
The router would make diagnosing much easier, like I said two NIC cards in a PC is a pain. I have setup PC based test systems both ways and the router option is well worth the extra $30. A router will also give you a better firewall for your PC and let you increase your highspeed internet bandwidth if connected to two or more PCs. If you do buy a router, it makes sense t get one with wireless as one without costs the same and most times more than one without. If you don't plan on using the wireless then don't go crazy and buy one with the fastest wireless, G will be fine and shouldn't cost much more than $40.00. Make sure it is a router/switch (most wireless ones are) and keep the recipe incase this doesn't work.
Remove the second NIC card from your PC. Setup the router per the quick install instructions that come with the router (PC to port 1, controller to port 2, internet from cable router or DSL box to the 5th or internet input port). When everything is setup you should get flashing LEDs on the computer NIC card and controller. You can interface the router through your internet browser by typing in 192.168.1.1 this should give you a window that asks for login name and password (listed in router setup usually something like admin password). This will pull-up a web type page generated by the router. There should be an option that allows you verify attached devices (attached devices, items on network, connected devices, or something like that) that will tell you the IP addresses of all items connected to the router (one will be your computer the other the controller if all is well). These are the two IP addresses you will need, if sounds like the controller will try to grab 192.168.1.50 as this is it's default. Your PC will be a static IP, which means it will grab what ever IP address is available every time the PC boots so if the controller needs a fixed IP to communicate with the computer we can set that later.
Hopefully this will at least get you 'talking' with the controller. This is how I would go about fixing the communication, hope it helps!