Hi,
The update improved a number of things for the Safari and made the theme inline with ios6, Apple unfortunately fragmented the ipad market for the first time, so now two separate versions of the code are needed to make pages display correctly in ios5 and ios6. The fix primarily dealt with that important issue, though not exclusively.
Ok, lets try this first, and depending on how it looks we will go from there. Please add this to the bottom of your Quick CSS, located in the backend : Choices > Theme Options > Styling - on the bottom of the page
.main_menu {
margin: 9px 0;
left: 25px;
}
@media only screen and (min-width: 768px) and (max-width: 989px) {
.main_menu {
position: static !important;
margin: 9px -40px !important;
width: 890px !important;
}
}
@media only screen and (min-width: 480px) and (max-width: 767px) {
select {
position: relative;
left: -235px;
top: 15px;
}
}
@media only screen and (max-width: 479px) {
select {
position: relative;
left: -315px;
top: 15px;
}
}
It would be a fine idea if they would throw up a dev.their-domain.com private development version of the blog, where these things can be sorted out without inconveniencing visitors.
We will deal with the indentation once we get this squared away , I started working on something after you first brought up the subject , though the colors and switch button are just there for testing, it could possibly function as an alternate drop-down menu for the mobile with indentation which you may be able to use. You can see it here http://jsfiddle.net/Nick_Wordpress/WQ7YH/ , but its a work in progress.
Please let us know how it went,
Thanks,
Nick
Create a new thread and tell me what problems you are encountering and what you want to know. 
There is no step 3 :) 
