Hi,
I'm sorry for the delay.
The problem with limitstart could probably be fixed by a simple customization directly in VirtueMart's code. If you know PHP you can try to add the following code to the beginning of /components/com_virtuemart/virtuemart.php file. Of course make a backup of the file prior to doing this.
if (is_null(JRequest::getVar('limitstart'))) {
JRequest::setVar('limitstart', 0);
}
I don't know why the URLs with virtuemart_manufacturerid were created. You could enable the URL Source Tracing so the information about its origin will be stored next time such URL is created.
It's very strange that the URLs contain the variable virtuemart_manufacturerid (with missing underscore before the "id" part). Maybe you have some custom URL somewhere on your website with this wrong variable?
Your 3rd problem may be caused by "Handle query variables as non-SEF" option being enabled in JoomSEF's Configuration on the Advanced tab. Try to disable it.