Recently I lowered the seat height on my Honda XR400R. It was needlessly high, adding suspension movement on top of the tyre diameter still left a lot of excess space. Shortening the sub-frame down tubes would allow the bolted on sub-frame to rotate downwards from the top mounting lowering the rear of the seat by a considerable amount, although not so much at the front area of the seat. Dropping the rear makes it much easier to get on and off the bike and I later removed about 30mm from the thick foam to lower the seat overall. For a 1.75m high rider (me) subsequent riding confirmed the benefit of the lower seat.
Original subframe showing where it was shortened.
Lowered subframe.
If only things were that simple. The lowered subframe meant that the air filter moved closer to the carb, but that wasn't a problem, the flexible coupling easily accepted that. The problem was that the airbox now fouled the shock. For obvious reasons I didn't want to move the shock so I had to cut away part of the airbox which leaves an entrance for water ingress when riding across rivers. I think that I'll have to make a new box in CF.
Another thing to fix was that the relationship between the subframe and muffler and its mountings was changed. I had to modify the muffler pipe to align everything again, not a big problem.
I found a short piece of steel tube in the airbox, it turned out that a cross tube on the top of the subframe had fractured due to a lack of proper bracing by Honda, and had fallen into the air inlet. In other words the subframe was not sufficiently rigid in a lateral direction. Continuous flexing had lead to the fracture. To improve on this rather than just replace the broken tube I welded in a diagonal bracing tube as well as a new cross tube.
Welding in the bracing tubes.
Cross tube and diagonal brace.