Adjusted the size now, all items fit comfortable into a 4x4metre square, and nothing exceeds 3m height.
About the rotation, there is an option in exporter "Fix up axis to Y", will try to uncheck this.
About the single commits, I tried to select all items at once and moved them over, but tortoise told me "this will be all single commits, wanna continue?", so I am not sure about to make a "packaged commitment". I could do a folder, but as all meshes are in one big folder and all materials in another, this doesnt make much sense then. Will check the settings of tortoise, maybe there is something wrong.
edit: This message I mean, my look in options doesnt bring up anything, will do a item-by-item commitment then until I found a solution for that.