If the problem is the use of reader macros foiling introspection by ASDF-JAR, then probably Fare's addition of :FEATURE to the ASDF system definition language is just what you need.
:FEATURE is evaluated at load time, thus not messing up ASDF's knowledge of what is and isn't "really there" in the system. So you could try replacing use of #+ with :FEATURE and see if that makes your problems go away.
I stumbled on this in a case which sounds similar: I was re-loading a system into a dumped image, and the semantics of the reader macros was all wonky, because they were interpreted at image save time, not at the time that I was trying to load the system....
HTH
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