I can usually find missing dependencies, but this one has me stumped:

An error occurred during custom object validation. (custdataset_sl_pf_cust_ship_sched_dataset)
Details: The object reference [scriptid=custcollectiontranslations_dataset_13_42aa992c5f714fa09da42.dataset_formula_32_2] is missing in the project and also not included in the dependencies list.
Details: The object reference [scriptid=custcollectiontranslations_dataset_13_42aa992c5f714fa09da42.dataset_formula_22_1] is missing in the project and also not included in the dependencies list.
Details: The object reference [scriptid=custcollectiontranslations_dataset_13_42aa992c5f714fa09da42.dataset_name_3_2] is missing in the project and also not included in the dependencies list.

Does anyone know how to find dependencies for SuiteAnalytics Workbooks and Datasets?

IIRC it has to do with translations. If you're not using that, you can grep the `custdataset_sl_pf_cust_ship_sched_dataset`XML file for translation and remove the elements.