I applaud your philosophy of trying to get things going even if not everything is in place - things never seems to ever get completely in place anyway :)
In terms of the difficulty of getting lab notebooks represented in a semantically rich format, some things are harder than others. The way I look at it, the easiest part of this is recording the log portion of experiment relating to what was done. We're simplifying the problems further by limiting our reports to the particular experimental design we're using now with vortexing vials and filtering products.
The bottleneck in all this is getting students to carefully convert their freeform writing into machine readable text. I'm not that concerned about the format we're using because we can always translate it to anything else quickly using a script.

Recording the interpretation of the experimental results is a much more challenging issue and I'm going to wait on that one until we do the low level recording properly first.