Hi Mike,
Thanks for the update.
I just want to clarify your problem.
You can use the EMIF Toolkit if you are using Cyclone V GX Starter Kit but you can't use if you are using your own custom board?
Can you provide the error that you are facing when linking the project to device?
In the LPDDR2 IP, are you already configure the Board Settings according to your own custom board?
Do you see any timing violation in the design?
Here is the link for LPDDR2 example design that you can refer to. There also a video that provides some explanation about the example design. https://community.intel.com/t5/FPGA-Wiki/TerASIC-LPDDR2-Example/ta-p/735535
Thanks,
Adzim