Trying to Join Bodies
Your model violated a number of recommended modeling practices for From (T-Spline) modeling.
1. You likely modeled this exclusively in smooth-view mode,. Have you looked at it in box-view mode? It looks very uneven and has self intersection geometry in several places.
2. There are triangles and many N-gons in the model. That seems particularly unnecessary in a simple model like this.
If you have a visual reference you are modeling this after, an image of video, then I can demonstrate how to model it.
Very nice! I t will take me a couple of days to get back to this. If you don't see a post from me, please tag me over the weekend.
The way I will likely pursue this is that I would create a few 3D fit-point splines (not more than4 spline points) and pull those into the approximate shape. Then use the T-Spline pipe command
This is what i have so far, but it means little without seeing how I modeled it. It just shows that this can be done 😉
You can see that all the tubular structures are interconnected in the T-Spline.
To answer your initial question, it is best to join the structures into one cohesive T-Spline and not afterward when they are converted into separate surface bodies. The video explains one way to approach to model this. It is almost 40 minutes long, so that shows that patience is needed.
But patience was likely also needed to create the clay model 😉
I the initial video I missed that this also did not convert. Here's the fix :
