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From what I've read custom messages are encouraged from the standpoint of showing would-be users of your work the API by which they may use what you've produced. More specifically, custom messages are encouraged to be provided in their own separate package so as to isolate them from everything else.
However I think you're on the right track. You should be able to use a pre-existing Float64MultiArray message without issues.
Here's the online documentation for it: std_msgs/Float64MultiArray Message
If I had to guess based on the code you published I would say that you failed to add anything to the "MultiArrayLayout" section of the message: std_msgs/MultiArrayLayout Message
Within that message is yet another message: std_msgs/MultiArrayDimension
Try poking at that. I haven't messed with the array-variants of the std_msgs yet, but it could be that the publisher isn't happy that one of those nested message types is empty.
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