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-Need to add Mission Objectives
This is done by having a text file usually with the extension ".otf" specified as the mission objectives in the mission's ODF file.
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-Need to add Units that will Patrol the areas
I'll try to explain it even though it's probably mentioned somewhere in the IA tutorial.
Load map in edit mode.
Press CTRL+A.
Press ESC, RESTART MISSION.
Press SHIFT+F9.
Press 1, 3. This will put you in "Edit Task" mode.
Click the object whose task you wish to edit.
Choose CMD_PATROL.
Click and then Right Click somewhere to activate the command.
Save the mission with CTRL+S.
I've never used the patrol command, so I don't know how well it will work. You can try it though.

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-Need help on making the Enemy Recycler and Factory actually build units
This is done with an AIP file with the same name as the BZN file.
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-Need help making the Enemy Constructers Build stuff
I don't think this is possible.

It would be nice though.
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-Need to add Nav beacons with names
I think it's possible to change the name of a Nav Beacon via hex editor (mentioned in IA tutorial somewhere) but an easier solution would be to find/create a Nav ODF with the name you want, and put that Nav object into the build menu, making sure it's Team 1.
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-Need to know how to Spawn enemy attack waves
I don't know about spawning them, but the enemy recycler and factory can build units and attack with them, as mentioned above, in the AIP.
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-Need to know how to do Airborne Infantry Assaults
This one might be tricky and I've never tried it myself. It would involve modifying the APC to hover really high, having it attack, then pause with CTRL+A and delete the APC, leaving the soldiers suspended in the air.