use of .shtml has issues tracking campaign IDs

That would be due to the redirect, not the file extension....

When pages are redirected, there is no tracking on those "initial touchpoints", only the final page that you land on (first, there's not enough time to execute tracking, and second, you wouldn't want to inflate your server calls by tracking each touchpoint in the redirection chain as PVs).

You should check with your development/operations team if they can forward the campaigns during the redirection.. 

Example:

• Initial Linked Page /initial.shtml?cid=x
  • extract ?cid=x and attach to the url that you are redirecting users to
• Redirected to Page /redirected/?cid=x
  • The ?cid=x is attached to the final destination

Or link people to the final URLs with your CID and not go through the redirect....  If these are legacy page to redesigned pages, then you need to build the campaign forwarding into the redirects, or accept that you will lose your campaigns until the new pages become the primary (and any old URLs that may get used will lose attribution <- this is sadly the state I have after our migration last year)