Hi Revolty,
Have you read this article?
http://forscan.org/forum/viewtopic.php?f=6&t=2
It has answers to all of your questions.
We agree the numbering is quite confusing. The way FORScan display the data matches to the one used in Ford dealership scanner and also it matches to the "natural" order the injectors data in ECU memory. But it is hard to read and hard to interprete, especially if you do it first time. We already discussed it with our users multiple time. There are examples of other implementation, for example Bosh KTS has no injector order, it only has cylinder order, so all codes are entered for cylinders. We agree this scheme is better, and the only reason why it is still not changed in FORScan is that this modification means quite significant modifications and massive re-testing on tens of models. This is quite large volume of work, we have no time for it right now.
Regarding firing order, please look at the picture carefully, at the cylinder order and injector order. Injector 1 cylinder
1 fires first. Injector 2 cylinder
3 fires next. Injector 3 cylinder
4 fires third. Injector 4 cylinder
2 fires last. So firing order for Mondeo Mk3 is 1-3-4-2 (as advised above).
Regarding of Mondeo TDCI pre-2003 - as explained in the article above, there is no way to confirm this except if DTC P233x was thrown. Changing code for right injector should remove the DTC. We have feedback from several users with Mondeo pre-2003 who programmed injectors this way and were quite satisfied with the result (DTC gone etc).