Mmh, it's hard to understand, what the problem is
After checking again and again I think, that I now know, what you mean.
And there is a very simple solution to connect your file 2.dat to the other parts. The bar above the tori is 5 LDU wide. Your 2.dat is 5.2 LDU wide. That's the main problem. I think you should recreate this 2.dat as a 16-sided version with 5 LDU diameter. If you need help while creating the cutout, just ask. This shouldn't be too hard for me.
Remember that you run into problems with the button again. You have to adapt its cutout to the new 2.5 LDU radius of the 2.dat content...
/Max
PS.: great work so far, that's exactly what we requested on PT.
PPS.: I still have some issues with the GUI-Version of ToriCalc. Just a hint: Please never try to input periodical decimals like ?.3333 or ?.6666 this will run the Commandline an endless Loop ;-)