The first Reference Design I looked at is a huge one. It has absolutely everything possible wired up, and "everything" is more than the CPU (and the other "everythings") can drive. So there are data and address buffers everywhere - about half of the board looks to be buffering. The RAM and FLASH chips are so big nowadays that you don't need that many of them, so unless you have strange requirements or a lot of I/O you can usually keep the design simple and do away with all the buffers. In that case you can probably use pull resistors on those pins. You shoudn't need jumpers if you know how you need the CPU set up. You know if you'll be using an 8/16/32 bit data bus for instance.
I always recommend stepping back from the current problems and reading the manual from cover to cover at least once, if not twice. You can skip the chapters for devices you're not using (like CAN or USB). At least that way when you are reading a section that doesn't make sense you have the chance of remembering "hey, that's explained better in this other chapter" and then search for that.
This is such an old chip that whatever problems you have, someone else is certain to have had before. And most likely posted about it in this forum. So use the search tools. Better still, search this forum with Google. It can often find things you can't find with NXP/s search. Do you know about limiting Google searches to a specific domain? Find out if you don't.
Tom