Approach it another way...
Make a solid component 'lump' that has the overall form, but without any 'holes'.
Then within another component add smaller solid groups/components that form the removal 'holes' - use Xray mode and section-planes to see what you are doing 'inside'.
Take care not to overlap or touch these parts, as that will compromise its future 'solidity'.
When you are happy with the arrangement explode that container's contents, it should then report as a 'solid' in Entity Info.
Then, use the Solid Tools to subtract that from the first 'lump'.
You now have the 'framework' as a new solid group...
You'll probably need to orient the faces so they are all 'outwards' looking...
Save as you go - using components allow you to reuse what was done before, without deep undo's...