If you can find a unique sequence within the repetitive region, then you should be able to find a primer. It might help to utilize LNA nucleotides (locked nucleic acids). They are nucleotides with higher melting temperatures than regular nucleotides and thus allow one to design shorter oligos for PCR, or to have leeway in your design specs. Perhaps you can utilize ePCR to check your designs.
Try using Primer BLAST: http://www.ncbi.nlm.nih.gov/tools/primer-blast/ Make sure you look at all of the options (scroll the page) as there is an option of checking primer specificity in a list of genomes of interest.