I am not very clear what you want exactly. But what I interpret is that you also want normal samples from fpkm files. Technically in the fpqm you have both normal and tumor data. While downloading the samples from GDC portal there will also be a meta data file under download option. Download it and it will link each sample to filename. There will be a TCGA barcode also given in a meta data file. That barcode will help you to characterise the samples. If you split that individual barcode by '-' the fourth element would be of form 01A,01B,11A,07A etc.
Note that this symbol enables you to identify whether it is normal or tumor.01-09 stands for tumor and 11-20 for normal.
Eg - barcode is if TCGA-P4-A5E8-01A-11R-A28H-07 then 4th element is 01A and is tumor whereas TCGA-P4-A5E8-11A-11R-A28H-07 4th element is 11A. Now if you look at the first 3 elements they are same meaning tumor and normal are from same patient.
The ICGC pipeline is explained in OICR wiki, if you have access to it.
It's the STAR 2-pass alignment, followed by HT-Seq count assuming all library are unstranded.
GDC is working on get all pipeline public (not in weeks, likely months), if you can wait.