I downloaded the zip. There is a lot of work to be done there!
The whole model is over 19,000 polys and over 38,000 tris.
The model is far too high poly for game design. I can imagine this is where your issue are coming from.
I would advise trimming a few thousand polys off the model and try it again. You can shave lots of polys off in the pipes. You could literally half the number by removing some of the edge loops.
Also, for that particular model, I would join all the pieces together and export it as one.
Give that a go and see if it helps.
Oh, I must say, I love the vision you have, the model has great shapes to it and looks very interesting. I hope you can get this sorted.
