Changed Auto Gearbox in 300tdi, now wont start??

I have just replaced the Auto box in my 300 TDI got everything back together now the thing wont start, we seem to have intermittent fuel issues, one minute its getting fuel the next its not, but when it is we have fuel at the injectors, the engine turns, but it wont start?? it seem like it wants to but something is stopping it?

We did damage a wire, that we discovered was popping the fuse on the fuel pump we have now fixed this and the fuse is no longer blowing, and all electricals seem fine apart rom the intermittent supply of fuel?

any help or advice would be much appreciated!