Specific as I mentioned "(virus file in use, can't be moved/deleted, etc.)," this shouldn't be too regular an coinsurance once you get your system in reasonable shape.
You obviously need to keep your browser, firewall, security software and OS up to date to reduce vulnerabilities (a problem with win98 no longer supported by MS), also not having XP you can't have the latest IE6 SP2 version. This should limit infection and reduce the detections in an on-demand scan, which would also limit the need to go into safe mode if a specific problem arose.
When I first tried to resize the window I'm sure that I was able to resize in vertical direction, having gone back to try it again, I can only get it to expand left and right. So that would appear be correct that you can't get the buttons in view.
So the inclusion of scroll bars would be a good idea so if the window size is less than the image background they would show and allow for scrolling to see the bottom buttons. If the window size were the same as the image size the scroll bars shouldn't display. Perhaps you should suggest this in the wishlist thread.
Have you actually tried to increase the screen resolution whilst in safe mode ?
It is a very long time since I last used win98se and I didn't have a high spec video card then but I'm sure that I got 800X600 on a 17crt monitor, now using a 20.1" widescreen TFT. What monitor and graphics card are you using ?