[Suicide Junkie]

TDM really only changes the AIs (Pictures\Races folder, data\formations, data\defaultstrategies)
FQM only changes the sector/system/galaxy definitions (data\secttypes, data\planetsize, data\quadranttypes, etc)
The balance mod only changes the racial setups. (data\happinesstypes, data\settings, data\racialtraits, etc)

If your destination mod does *not* change those files, then you can splice them together without too much trouble.

*Note: TDM won't work if the destination mod changes the gameplay too much. TDM AIs expect components, hulls and facilities to be similar to stock, and the scripts will be fubar if those are changed significantly. Small changes can be handled, though.