What aspects of ACT-R are not contained within Spaun?
Both ACT-R and Spaun are modular, and could be extended to include capabilities of each other. Comparing the functionalities of the two architectures by a simple checklist is not the most appropriate way to compare them. Here are some points to consider:

1) ACT-R is primarily symbolic, whereas Spaun is a neural network. ACT-R is actually making a theoretical claim by committing to a symbolic architecture. This is one of the most famous debates in cognitive science; the upshot is that the two approaches each have limitations, and they go about solving problems in different ways. For a good starting point in this debate, see Fodor &amp; Pylyshyn (1988).

2) Architecture aside, different algorithms can be implemented to solve the same problem. Maybe both Spaun and ACT-R can do simple declarative memory retrievals, but do they predict the same response times and accuracies for a given retrieval? I suspect they don't.

3) As mentioned in your answer, Spaun does not include a of long-term memory but does include working memory. In ACT-R, long-term memory and working memory are not distinct concepts; working memory can be construed as a subset of items in memory that are highly activated. There is no discrete distinction. This suggests that the structure of components in ACT-R is fundamentally different than Spaun.