Hello and welcome !
I have the same car as the one you are interested in, so will do my best to help you with your queeries -
1) The post '06 upgraded screen and nav system are great, imho. It doesn't have full post code search and only you will know if this will be a problem for you. Save for looking for commercial premises without numbers and sports facilities on long rural roads, I haven't found it to be a problem.
2) Yes you can - for about £140. Cheap Toyota Parts is one of the best places to get them. Alternatively, if you go for a Lexus Platinum Care package for future services, you will get 10% discount from the dealership.
3) I don't have an iPhone, but I have seen several posts on here commenting on varying degrees of success with paring and functionality. A Forum Search for iPhone should provide you with some useful information on this.
I hope that helps.