Can anyone help?

I recently bought a 1.8 Scirocco Scala, unfortunately it need a new engine which i purchased from an auto breakers. The old engine was a:
DX 112 1,8 08 / 83 - 07 / 92 Scirocco K - Jetronic,

The new one i was sold was one of:
PB 112 1,8 03 / 87 - 10 / 91 Golf , Jetta Digifant
PB 112 1,8 04 / 88 - 07 / 90 Passat Digifant

Due to the different injection systems we used the new engine as a short engine and kept the original head, but swapped the cam shaft due to the new one being in better condition.

After a lot of hard work it is back together however no-one seems to be able to set the timing and although it is running timed on #3 140° out at the minute it is a long way from driveable!!!

We have checked the top sprokets both have the same number of teeth, and we are now running out of ideas!! As far as i was aware swapping VW engines around was supposed to be easy!! If anyone has any ideas of where i can go from here, or if you think you know what the problem is please contact me.

Cheers
Absolutsteve