Hi Brad,
Following is the code to enter multiple value lookup. For every selected value from Lookup we create new customfield and assign the Lookup's LT_STUCT_UID to the newly created CF.
SvcProject.ProjectDataSet.ProjectCustomFieldsRow cfRow = currentProjDs.ProjectCustomFields.NewProjectCustomFieldsRow();
cfRow.CUSTOM_FIELD_UID = Guid.NewGuid();
cfRow.PROJ_UID = new Guide("e6ddce9e-0867-406f-bdcb-f0b4a94ffd8f");//Project Guid
//Following information can be obtained from [MSP_CUSTOM_FIELDS_PUBLISHED_VIEW] view
cfRow.MD_PROP_UID = new Guide("DD0A5445-D2FB-4E42-B4EE-D05D8B5704A4");// Prop UID
cfRow.MD_PROP_ID = 190873618;
cfRow.FIELD_TYPE_ENUM = 21; //21 for Text value
//For Lookup table
cfRow.CODE_VALUE =new Guide("67f8adf8-a441-4231-bfb3-b21c4d943705");//LT_STRUCT_UID;
Hope this helps you. In case you still face issues let me know.
Thanks, Kashif