Sorry I didn't get back to you sooner.
If you reconnect the factory deck, the small grey cable in the trunk is already supplying a low-level signal. All the bypass harness is doing is saving the connector on that cable.
After re-reading your posts, I think I may understand better what you're trying to do. You're trying to reinstall the factory head unit, and still use your amp to power the subs. The problem with that is that the factory head unit only has low level outputs--it cannot drive your speakers without an external amp. If you still have the factory amp and the car's wiring is intact, I'd recommend basically reconnecting the factory setup and doing without the subs until you get the other head unit back. Otherwise, you'll have to connect the factory amp, then splice into the car's wiring in the trunk to be able to feed a crossover to split the signal to the 4 speakers & subs.