Hi, Sam! Welcome to Wikitree. I'm not too familiar with GEDCOMs but I do know that they expire in 30 or 60 days. You may want to divide you tree into a new, smaller GEDCOM and try again.
Many report that it is actually easier to simply create profiles directly as the compare process takes time and then each profile added will need to be cleaned because the data is transferred with a lot of garbage. When you create them anew (or edit them if already here), you have a chance to ensure they are properly sourced.
Additionally, once you have completed maybe three or four generations, you are likely to find the profiles are already on Wikitree and you can just edit to add anything extra you have found.