Unity5 Z sorting problem, urgent!

So… i’ve had to upgrade the project from 4 to 5.2 version of unity. After all the 3d modelling and baking is done, i started to do final tweaks to my shaders. The Unity4 project was very complicated with crossfades between industrial objects and things like semi-transparent tubes with a semi-transparent steam schematic inside and cutoff schematic outside, but i’ve managed to get it to work perfectly. And now i’ve got 3 days until deadline and i’ve found that all the same models and shaders do not work in Unity5. Ugly transparency issues, z-sorting problems and non of the shaders work. Custom, built in - no use. I’ve tried everything - scaling, changing rendering mode, all sorts of transparency settings. Yes, i know that the depth now comes from shadowcaster. The best result is correct crossfading with ugly sorting problems during the crossfade.
What do i do now? How i can even try to predict my work terms if i encounter things that worked and now broken?
I don’t think it will be any help(color animation ticket is like 3 years old, for example), but it would be great if someone has a solution. It seems like i’m gonna get penalty because of this.

What was your reason for upgrading? It’s pretty risky to do a major version change of your software three days before a deadline. Can’t you just roll back?

I’ve been given a month to get an old app from Unity4 to work on a newer devices and plug-ins(android3 just released when the first app was made). I just did all the correctives to textures, updated some models(not theese that causes the problem) and when everthing was almost ready i started to do some final steps. Also, the task was to keep most of the original app. It seems like the “optimization” of the render pipeline in newer versions of an engine causes lots of issues. I’m just really upset because most of the development time i’m not working, just fixing problems and search for workarounds of issues that shouldn’t be there in the first place. I can do some weird stuff like swapping materials and shuffle crossfades so the transparent objects would come fading in front of the opaque ones. But all of this is weird and it’s really crappy that i have to do all this stuff instead of sleeping(it’s 4am in here right now), for example.

Sounds like the original shaders were probably doing some tricks to make the depth sorting work. The built in shaders don’t really deal with transparency on complex models will.