Assemble with the BPW so you can see how much bolt sticks above your speednut. Use a hacksaw/sawzalll/multi-tool to cut that much off the bolt and clean up / lightly round the corners of the end with a file. No need to disassemble the bands.
You can certainly do it that way… And if they’re excessively long, and I had everything else positioned exactly where I wanted them to be but there was still too much bolt left, that’s pretty much exactly what I would do.
However, if that truly is threaded rod (and not a bolt) on your tanks, I very much dislike the fact that you have the back nut, a nut that is critical to holding your bands together, without at least a few threads sticking out past it. It’s way too easy for that nut to come off. Therefore, I think you need to shift that entire rod back some no matter what, even if you then decided to cut some of it off.
If I were asked to do it, the way I would do it relatively simple: loosen all three nuts on that all thread a little bit (1/8” or so), re-tightening them in such a way as to shift the all thread where I wanted it to be, then tighten all the nuts back up. Basically, that means loosening the top annd middle nut, and then tightening the back nut up, then loosening the top nut, etc. I wouldn’t touch the manifold, nor would I touch the bottom band. Be very careful and don’t move the tanks around, and you’ll have no problem adjusting that rod to where you want it to be.
Personally, I am not a fan of putting a nut inside of the two bands. That’s mainly because it makes operations like this one very difficult. It’s difficult to get a wrench on that nut, and because of that, most people put that nut in place and then tighten everything around *that* nut. What that means in practice is that unless that nut was put exactly where it needed to be right from the beginning, you get exactly the situation you have: the rod is in the wrong spot, and it’s difficult to fix.
I haven’t seen any arguments why having that extra nut there is valuable, anyway: there’s still stress on the back half of the band, so I don’t see how it’s really relieving or securing anything. Now, if you used four nuts, one on each side of the two pieces of the band, I can see how that would hold everything in place while needing a little bit less stress on the bands. But that’s a really big hassle to do. And with modern bands with the extra thick spacers welded in, I just don’t see any value. If someone out there can give me a good reason I’m open to it, but I haven’t seen it or experienced it.
Anyway, once you finish the top band and get it tightened back in place with the bolts being the right length, you can repeat the process with the bottom band.
ETA: a trick I just recently learned from
@coleman.jamie: with all thread, you need a way of being able to grab the rod when you’re loosening or tightening things. In the past, I just picked an out-of-the-way spot and grabbed it with channel lock style pliers. Yes, it chewed up the thread, so I always made sure I had a nut where I could re-chase the threads with it. Yes, not at all the way it should be done.
He showed me that if you take two nuts and thread them on the threaded rod a bit and then tighten the two nuts against each other, you could then use those nuts like the head of a bolt and the threaded rod would stay in place. Simple, and preserves your threads. So I thought I would share. Once you say it out loud it’s so obvious and simple, but I had never seen it before, so hopefully that’ll help someone else from screwing up their threads.
ETA2:
That said, none of my double have a bolt between the bands. Which is fubar because it stops the bands from being tighten fully. There is also no lock washer which is really fubar.
I missed this the first time I read it. I already mentioned the fact that I don’t put a nut between the bands, either: nice to see someone else agrees with me.

That is, assuming you wrote “bolt” when you actually meant “nut”.
I too noticed the missing lock washer. But I’m not a fan of lockwashers. I’m much prefer Nylok self-locking nuts. And I would very much recommend that you add them here.
Honestly, given the large amount of questionable choices demonstrated here, I honestly think I would consider completely redoing everything. The entire look of this assembly gives the vibe of being put together quickly, and doesn’t give me a great deal of confidence. Someone else mentioned making sure that the center isolator is not under strain. That can sometimes be easy, but sometimes can be surprisingly difficult, especially when you’re using bands not designed for this size tank as you seem to be here. It ends up taking more than a little bit of adjusting between the isolator position and both sets of bands. I’m not certain that that was done here.
Anyway, you asked a specific question, and I tried to give you a specific answer to that question. But I would consider that you consider the entire assembly as a whole and decide what’s best for your situation.