Well, the minimum reasonable length of bellows is just enough to handle vibration -- call it a few inches. You are off the charts as far as (lack of) conductance of your plumbing goes. At the pressure levels involved, you are no longer talking about pressure -- where existing gas molecule collisions "force" other molecules into the pump. You are getting into molecular flow, which means that you are just waiting for them to find their way in there at random, which takes a lot longer -- the gas molecules rarely "hit" one another at that point. So, no, skinny copper pipe will only help with surface area to outgas, but not so much pumping speed. This is why you see 6" and larger pipe on all high vacuum systems, and usually short enough that you can see through it with maybe 30 degrees off axis viewpoint. Sad, but true.
For the bypass system, this is fine (once you outgas it) -- you
want slow pumping via that loop for when you're trying to balance a slow deliberate gas inflow with a slow (and about equal) pumping speed. For getting there in the first place, even a foot of 1" bellows might be too much, particularly since you're trying to get near the limits of the pump in question. I have for example a 4" long by 6" diameter pipe between my final pump and my system for the big system, and well under a foot of 4" pipe for the small one. And the small one gets to e-5 where the big guy gets to e-8 in about the same time...That's with no leaks at all, just outgasing. Once you've got your bypass line "clean" then just ensure it doesn't have to go to STP everytime you open the system -- a valve here and there helps with that, so you never stop pumping on things like that if you can help it. Filling the tank with dry welding gas when you have to let it up to atmosphere does help and argon is a good one for that -- it's dry and doesn't "stick" so well to the tank and plumbing walls as say, water does.
See how it does with the main pumping scheme operating overnight (not just the bypass), that will tell a lot. And maybe whether you have a leak too. One way to tell is with more sensors, you might find my cheapo pirani sensor project worthwhile. For example, if you put a sensor right on the pump, and one on the tank, and then close off the pump valve and the pump sensor goes way down -- you know the system has issues. If the sensor at the pump is always reading much lower than one on the main tank, then you also know that you don't have enough "conductance" to get the job done. These are cheap to make, so you can afford to have a few of them here and there on your system, and it's very educational. I can give you a few of the sensors (grain of wheat bulbs, hard to find, so we bought hundreds when we did).
All that junk in the path limits your effective pumping speed a lot. As in orders of magnitude. You can probably find speed vs pressure curves for your pump (or one just like it) at
Leskers website too. And note the funny units they use to handle the case that at lower pressures, you're not pumping as much actual gas as at higher ones.
I tell everyone to sign up and get the free Kurt Lesker catAlog, the old print version of which has a better section on all this than the document below -- but this is a start. You have to get it in your head that this isn't just water flowing through a pipe, and that you can get it all in a couple minutes of pumping. As you get close to the area fusion happens in (long mean free paths) a long skinny pipe may have more or less zero flow -- not enough pressure drop between an assumed perfect vacuum at the pump end and the millitorr at your chamber exists to "push" gas to the pump, and in the case of molecular flow, it's not "pressure" at all -- just random chance a molecule will bounce it's way into the pump (and not just bounce back out).
However, I suspect you still have a leak. Most outgassing should be over with overnight, at least using the main pumping line (short, fat, shiny).
You can try this:
Bake the system. You can use heat gun, IR light, heat tape, whatever. At first turnon, that should cause the pressure to rise, and plateau. Then, it should slowly drop back to and even below what it was when you started out -- this may take hours. Then turn off the heat, and you should see the pressure drop further. If not, you've got a leak still. Raising the pressure via heat sounds dumb at first, but it's not -- it's making it easier for the pump to remove the junk off the tank walls -- and sans leaks, once it's gone, it's gone, which is why after cooling, you wind up with less pressure than at the start.
If there's no viton, you can get the system pretty hot (a couple hundred C) without harm, if there's viton, keep it to 100 C and wait (much) longer. Don't skip heating anything in the vacuum, including all the hoses up to the tank (but be careful about overheating valves that have viton or plastic in them).
Posting as just me, not as the forum owner. Everything I say is "in my opinion" and YMMV -- which should go for everyone without saying.