Ok. I've been modeling for quite a while now, and I've tried out many 3d apps, including TS 3.2, 5 and 6, Blender, Lightwave, Milkshape, 3ds Max, gmax and even DOGA. They all have their strengths and weaknesses and all have their own sets of techniques that work and don't work.
So
please believe me when I say that TS 3.2 is probably the biggest problem both of you and many others have at this time. In fact, I don't know of a single person on HLP who has produced even a moderately detailed ship using only 3.2.
The program is simply incapable of producing stable complex shapes! Even the simpler things that would take minutes in a normal app can take ages in 3.2.
As such, there is
no reason to be relying on it as heavily as a lot of new FS modders do. It's like trying to learn to fly a helicopter by riding a bike. You'll never get off the ground.
Saying 'but it's free' is no excuse either.

Blender and possibly Wings3d will be along shortly to beat you to death with a trout. If you want a totally free and legal way to do 3d modeling for Freespace, you barely need to use TS 3.2 at all.
ALL you would actually need it for is to set up the heirarchy of all your existing and positioned objects, scale the whole thing and then to save it as a COB/SCN.
I know I must sound like a broken record when it comes to TS vs Blender, and please don't think I'm attacking anyone, but I just get so tired of HLP modders getting stuck on 3.2 when they don't have to be. Many such modelers have given up modeling completely, no matter how much potential their designs show. 3.2 just strangles them with problems of every kind, and gives them next to no real modeling power in return. Modelers should be limited by time and imagination. NOT their chosen program.

For example:
If a ship converted before to .pof but I had to break it up in order to cleanly edit some stuff out and now am stuck with 52 objects off one of 5 main parts and it fails conversion cause of this, HOW can I merge all those objects into one part again? (Using only ts3.2) is it possible? I tried union but nothing happens.
In Blender, you would shift+right-click select all the objects you wanted to make a part of the same object, and press ctrl+j.
In 3ds Max you would just select one object, click 'attach list' and select all the objects you wanted to attach in a nice neat list form.
How do you do it in TS? Well first you will need to make sure none of the objects are inside each other and that they aren't touching each other anywhere. Then you select one object, select the boolean union tool and proceed to boolean every object together one at a time. Be careful on the order in which you select them or you might put one of the yet-to-be-attached ones inside the bounding box of the attached ones, which has caused headaches before. Also be careful which ones you click - TS doesn't always go for the one you click on. If there was something behind it, more often than not you will grab it and not the object. Aside from that, it's good to save right before trying this whole operation because TS will very often crash at seemingly random ones, and the undo only undoes some of them some of the time. Be sure to save right afterwards as well. Once that's done, if any objects were in or touching each other before you moved them, you'll now have to border-select all their verts or faces and move them back into place.
And no I'm not talking about simply gluing objects together. That does not join them into one mesh object as the method I've described will do in each program.
As I've said in many of my previous broken record loops, if anyone out there has a simpler method for doing the above in TS 3.2, then please let me know!