Hi Patrick,
Yes, we had huge customizations on almost all the JSPs you mention above as well as close to 300+ additional java classes and as well as many modified standard SAP java code. All these over many many years of development.
ISA7.32 is no different from ISA 5.0 technically except that it runs on JDK6. Functionally there are a few extra features like Loyalty Management.
The biggest hurdle we had was about the changed signature of methods of standard Java classes and some classes even deleted from packages in the newer version. Any custom java classes using these classes/methods had to be adjusted.
With similar/more enhancements to what you mention above, upgrading the entire codebase to the newer version took us around 60 days of effort including the fresh setup right from the SLD upto the new J2EE engine and doing the code conflict merge.
The approach we took was to take all JSPs from the 5.0 version and overwrite the 7.32 version (as it would not make much sense to rewrite them) and for the Java/XML files we did a compare and merge approach.
Regarding the backend RFC calls, most of them remain same in the order/basket area. I had noticed some changes in the contract items piece where there were now additional import/export parameter and some were even not optional forcing us to send some dummy values where necessary.
However, if you are using the variant configuration functionality in ISA you will be in surprise. The old ISA 5.0 IPC configuration will not work in 7.32. The newer version has something called as a decoupled mode (for performance reasons) and we had some challenges in that area to get the entire IPC working well. However if you use IPC only for the pricing bit, not much to worry as it remains mostly same.
PS: We were running a B2C scenario and not B2B. B2C is much more complicated.
Hope this helps.
Pradeep