re popup:
without a link , I cannot tell you anything

re backup: i cannot help you. it is your backup solutions responsibility to transfer things correctly / completely

a few things:

generally: ignoring a couple of css declarations (mainly distinctly setting cursor:pointer for a few elements) there is no code anywhere that distinctly targets iStuff or non-iStuff, so it does not make much sense to me when you say that some things do not work on your iPhone (but i cannot speak for any other plugins or the theme you are using as those might of course change things)

> Pre-order: 15 minutes before the closing is not working! You can place orders until closing time.
you will always be able to place orders when you are actually open at that time (otherwise there isn’t really any point of having the shop open at that time in the first place) , the “15 minutes before closing” only applies to preorders in/for the future (i guess i could make this a bit clearer perhaps)

>Pop-up with Iphone is problematic.
>but height remains small and you can not scroll down.

in the past – with very old versions of the plugin – perhaps. if that were still the case, I am sure I would have heard about it. Moreover, from what i can see on your site this works just fine. I cannot see the problem you seem to be having to be honest. Have you tried a different phone ?
have you tried disabling all other plugins using a default theme ?

>Ingredients pop-up does not work with the long list but with less decay already.
Sorry, but I don’t understand what you are trying to say