Hi,
1) As regards the first non-SEF URL:
/index.php?option=com_content&view=article&id=75:frangipani-plants-how-to-prune-plumeria-rubra&catid=16:plant-garden-care-blog&Itemid=171
It should be automatically redirected to:
/plant-garden-care-blog/plant-garden-care-blog/frangipani-plants-how-to-prune-plumeria-rubra
by JoomSEF, so Google should just stop reporting it after some time.
For different SEF URLs like:
/shop/all-nursery-plants-for-sale/philodendron-imperial-green
and
/shop/buy-exotic-tropical-plants/philodendron-imperial-green
you can manually modify your meta tags using JoomSEF's URLs Manager.
However for SEF URLs with some non-SEF variables like:
/shop/buy-exotic-tropical-plants/philodendron-imperial-green?limit=int&limitstart=0
or
/shop/buy-bamboo?limit=2&limitstart=0&orderby=product_price&order=DESC
you can't set different meta tags in JoomSEF, but you can check if you have automatic canonical link generation enabled in JoomSEF's Configuration on the Advanced tab (it should be enabled by default). That way JoomSEF will generate the canonical link to the pure SEF URL, so Google should know that it's preferred.
You can also use the Options -> URL Parameters in Google Webmasters Tools to set up non-SEF variables that should be ignored.
2) To automatically redirect URLs starting with /~lushplan to their corresponding URL without it, you will need to create custom RewriteRule for mod_rewrite in your .htaccess file. For more information about mod_rewrite see its documentation at:
httpd.apache.org/docs/current/mod/mod_rewrite.html 
