We went through all these issues with ours- chopping the top to keep us under 13'6", shortening the container (we didn't want that much box swinging behind us when turning tightly), chopping the bottom to eliminate the empty space below the container's floor, cutting and bracing door and window openings, fabricating a rear door that could withstand substabtial weight when folded down as a drawbridge, and so on.
In the end, there would have been so little of the original container left untouched, that we decided to build a composite wood/epoxy box.
And we would have had to build a wood box inside the container anyway, as we built the interior.
We also were never able to adequately solve the condensation issue with a steel box- anywhere that humid air (your breath, shower steam, cooking steam, etc.) touches the inside of that steel box, water is going to condense on it and you'll have mold inside your walls.
With our wood/epoxy box, the walls are completely filled with 3.5" rigid polyiso foam insulation (R-24 value), foamed in place with urethane insulation foam- there is no airspace in our walls, at all, even around plumbing and wiring, so there's no way for humid air to get in, and even if it did, there's no steel outer skin for it to condense on.
As far as our headroom- we've got plenty. You can do the math, but our box is 5" thick on all walls, so if you take your box height (which is about the same as ours) and subtract 5" for the floor and 5" for the ceiling, you should come up with about 6'8" of headroom...
