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Some minor suggestions (1)

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This is looking great, it is a difficult figure to replicate. A few suggestions, maybe these are already planned:

Following SPE should be "pro-Spatzle". Even if it is a precursor with an unknown (or no) identifier, you can add it to the pathway as a label.
For the intra-nuclear portion, all of the relevant proteins (Dif/Dorsal, Relish, Stat) should be represented there as well. You can also add a mim-transcription/translation interaction for each, which would link to each of the genes that are transcribed (TEPs etc).
replace JNK gene node with a "JNK signaling" pathway node.