According to this study Autism has gone up, and quite a bit - Prevalence has increased by 6-15 percent each year from 2002 to 2010. -
https://www.cdc.gov/ncbddd/autism/data.html
EDIT: misread your post, we're not in disagreement here.
However I don't see any evidence that thimerosal was removed from childhood vaccines, just a 1 liner in your cdc report that also says there actually still is thimerosal in flu vaccines (and 4 out of 7 of those vaccines)
edit: it's actually 4 out of 8 flu vaccines, but 4 out of 7 trivalent flu vaccines.
Considering flu vaccination has been steadily on the rise, its a good idea to look for which vaccines are used the most.