I am looking for a mouse gtf to run with cufflinks that includes data on genes, isoforms, promoters, cds, and tss. So far, I have only been able to locate a gtf with data on genes, isoforms, and cds.
GTF is a gene transfer format and as such it is supposed to be limited to describing genes. You may be able to coerce other features to look like genes but I think there is a chance that this would invalidate the results of some of the tools and techniques that you want to employ later. Those too may have been built to expect input from genes.