Importing a mysqldump from MySQL 5.0.95 to MariaDB 10.0.36: Some tables incomplete
5.0 -> 5.1 -> 5.5 -> 5.6/10.0 -- That's 3 major upgrades.  Various tables in the mysql database have been added/changed.  Lots of changes to information_schema / performance_schema.

You would be quite lucky to leap from 5.0 to 10.0 without some major hiccups.  You did run mysql_upgarde?  MariaDB tries to make that handle multiple hops, but this may be more than it can handle.

if enforce_storage_engine is turned on, this could explain the sudden appearance of unexpected .ibd files.  There can be hiccups in blindly changing the Engine.

How are you measuring number of rows?  When using SHOW TABLE STATUS, MyISAM has exact numbers; InnoDB has approximate numbers.  Even 307 versus 4000 is not unheard of.  Use SELECT COUNT(*) .. to be sure.

As for the empty table -- manually run the load for it; see if you get any extra clues.