Hi,
1.) I guess you've set "Use Bootstrap design" to yes, but your template is not built on Bootstrap. So set it (back) to no and save, and all should be good again with columns.
www.hikashop.com/support/support/documen...html#display_general
2.) That's maybe due to you having canonical URLs enabled, and some meanwhile obsolete URLs still being in the system. An easy way to test is turning off the use of canonical URLs, at least for the purpose of testing: set "Force canonical URLs on listings" to "No, generate the URLs" and save, then check the frontend. If that fixes it but you want canonical URLs, you'll need to check/empty/change all related fields in categories and products before enabling canonical URLs again. You can do so manually, or use a mass action if it's many, many items.
www.hikashop.com/support/support/documen...ig.html#features_sef
(screenshot outdated, text ok)
www.hikashop.com/support/support/documen...massaction-form.html
(careful with it, complete backup incl database first!)
3.) Double-check your settings for "Product page image width" and "... height". You may want to increase the values there. As the name implies, that's for the product (detail) pages, while the thumbnail settings are for listings. Needless to say, make sure that the uploaded images are large enough, and that "Image width" and "Image height" are not too small, either.
www.hikashop.com/support/support/documen...fig.html#main_images
4.) That's well possible - not for "options", but for "characteristics" which result in "variants" of a main product, depending on your settings. For something like color variations of the (same) main product, characteristics are the way to go for creating (color) variants for which you can use and display different images. You may also want to look at the tutorial for "display by color".
www.hikashop.com/support/support/documen...html#characteristics
Since 2.5.0 the product add/edit page in the backend has changed, but characteristics only became simpler:
www.hikashop.com/support/documentation/i...oduct-interface.html
And then eventually
www.hikashop.com/support/support/documen...isplay-by-color.html
Not only due to the given great flexibility and fast development/improvements of HikaShop, some fiddling a.k.a. trial & error will always be part of the game, I'd say (me = being user like yourself). Helps understanding how things work, and probably you'll get to see more of the possibilities than by only reading long manuals and "following orders". 
Also, I guess we need to forgive the HikaShop team if the documentation is not always totally up-to-date as, again, this drawback is easily outweighed by the fast and vast addition and improvements of features. That's at least my 2 cents...