There is a way to get some things working: editing the .skn file. In your project directory, find the skin in the !SkinSubFolder! and open the <skinname>.skn with a text editor. It is just an XML file so you can make some changes there.
Find the two occurances of cold="220,*" and amend the first number to your liking to set the sidebar width. Save it and generate your output.
If I'm not mistaken, the size for the search field can only be set by mucking about in the output files. After you've done that, make a copy of the modified files and paste them in the output every time you generate. That may save you some time. Rick's Skinny on Skins should have the instructions on setting the size of the search field.
Yes, thank you, you are right. Actually, I found I only had to make that change in the output one time to my liking, and it did not overwrite those changes every time I generated. It ended up not being the pain in my neck I thought it would be. That fixed my problem with the books not showing up on the far left and having to scroll to see them, too.
Whew, huge time saver! Thanks!