Not quite... read carefully what he said. It is a direct linkage to the front driveshaft, not to everything else. Your Automatic Disconnecting Differential (ADD) uses vacuum pressure that actuates the front differentials drive of the front axles. The only thing your manual hubs allow you to do is unlock the hub from the front axles.

For 4x4 to work the following must be in place:
1) Lock your hubs. Trying 4wd without locking the hubs is ill-advised. Before you put Aisin's on, you had a flange plate that essentially was a permanently locked hub
2) Pull your 4wd shifter. This engages the transfer case to the front driveshaft.
3) Vacuum pressure engages the front axles (this is done via a switch connected to your shift lever). If for some reason you are not getting vacuum pressure then the light doesn't come on and you don't truly have 4x4.

Does that make sense? I'm not totally sure why fussing with the 4wd shifter finally makes it work for you. But for some reason you aren't getting vacuum actuation (either because of a vaccum leak, switch malfunction, etc.)

Good luck,
Joel