> I'm trying to create a RNA-Seq Workflow with Bowtie/Tophat and Cufflinks 
> using a newly assembled genome (not public).  I created the genome index 
> files via Bowtie locally but Galaxy will not accept the .ebwt index files 
> (n=4)--"Inappropriate content" error.

Galaxy will not accept Bowtie indices. When you provide Bowtie/Tophat with a 
custom genome via Galaxy, Galaxy will create the indices needed for the tool to 
run before running the tool.

> Second, for some reason, the Illumina fastq files will not load on the web 
> version or my local version either.

You'll need to groom the files to convert them from fastq format to fastqsanger 
format, which is the format accepted by Galaxy's NGS tools. See the 
FastqGroomer tool for details. (If you're confident your fastq quality scores 
are in Sanger format, you can simply change the fastq dataset's datatype by 
clicking on its pencil and looking for the datatype selection on the page. This 
will take less time than running the groomer.)

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