I've got the TT Humongous Bazookas, since I figured more room is better.
The Gitzo you've got is similar in size to my Feisol CT-3371. The Humongous will fit that tripod with a Wimberley v1 head attached. It's a tight squeeze for the head, but the legs still have lots of room.
i don't use padded bags. tripods are bulky enough as it is and really don't need that level of protection. i use a simple kinesis gear tripod bag anda kinesis ball head bag. if i feel padding is required someday i can simply add it. i have both gitzo and feisol tripod and will have an RRS soon enough. i am currently shooting in Beijing and got here just on sunday. just got my first unexpected snow too.
The Gitzo GT3541LS will just fit in a regular ThinkTank Bazooka with no pads on the legs. The bag takes on a slightly triangular shape when you have a tight fit, and I like the fit that way. The inside of the bag is smooth, and the tight fit still allows you to put the tripod in and take it out easily. I would guess that the Big Bazooka would be just right for your tripod with leg wraps. You did not say if you have a thin tape like wrap, or a thicker padded set of leg covers, but in either case, I think you will be fine. If you use my reference of nice and tight but works fine with no leg padding for the regular Bazooka at 5" inside diameter, and the Big Bazooka is 6" diameter, you should be able to judge if the Big is going to work for you. Remember that the largest part of the head is about 1/2" larger diameter that the diameter of the legs where your pads are. So the first 1/4" of pad thickness will not count toward bag fit.
I have great things to say about the ThinkTank Bazooka, and have been using and abusing mine for almost three years now. I like a firm fit on the inside, and the Bazookas can be adjusted to fit the length of the tripod and head that is inside. That keeps the tripod from "rattling around", which I think is great. The padding on the sides and top and bottom protects from the ordinary dings and scratches very well, and protects the head also. In a photo workshop environment it is easy to throw your expensive tripod and head in a pile with other tripods, and not worry in the least. I have put an even better padded strap on the Bazooka than the one it comes with, and often use that to carry my tripod on mid length day hikes along with a shoulder bag for my camera.
