Bally
Yep, verified the correct switches selected for the game, also cleared the Altek's memory.

Did a switch test and had some odd results, i found that the switches from number 21 onwards corresponded to the manual, with the exception of the ball kicker which is switch 35 in manual but switch 34 in the game.

Switches from 10-20 did not correspond to the manual whatsoever...
For example
Switch 10 yellow drop target was actually sw02 in game
Switch 11 blue drop target was actually sw02 in game
There are more examples of this throughout the game...

So i started doing a switch matrix verification and have noticed that for the most part ST2C, ST3D, ST4E matrix colours all reconciled however ST0 and ST1, in particular chute and drop target wiring has been messed with.

The drop target assembly has the common ground wire removed on the last target, and wires are missing on some of the switch lugs corresponding to the switch matrix....

I assume that because ofnthese issues, the MPU is registering some of the switches incorrectly and hence the switch number reconciliation issues...

OK, carefully go through the switches and try and return them to their correct state.  Look for: wires removed, particularly if this breaks a 'daisy chain'; diodes missing or incorrectly oriented; broken diodes, wires not in the right place.  

Also, carefully go through the connectors on the MPU (J2 and J3) and make sure all the wires are in the right place - people will swap them and this causes all sorts of grief!

When you say the common ground was removed from the DT, do you mean the power wire?  If so that has no impact, but was probably removed due to Q11 always blowing.  You can easily disconnect the whole target bank by unplugging it and seeing if the rest of the switches then read correctly, and if so you have isolated the problem.

Hang in there - it will all come together