Auto-immune link?
I don't think so. From the pdf:
"Environmental perchlorate exposure is of potential health concern because much larger doses of perchlorate have been shown to competitively inhibit iodide uptake (Greer et al. 2002; Wyngaarden et al. 1953). Populations with low intake of iodine or increased demand for iodine may be more vulnerable to inhibition of iodide uptake. Sustained inhibition of iodide uptake can lead to hypothyroidism, although perchlorate-induced changes to thyroid function have not been previously demonstrated in any human population exposed to perchlorate, even at doses as high as 0.5 milligrams per kilogram body weight per day (NAS 2005)." Page 7