I have recently returned to GMing T2K, and started with the original storyline. I do give the players a completely free rein, and give myself headaches as a result
Anyway, after much detouring from Kalitz they finally arrived in Krakow more from realising via intel that it was the only safe place to go at that time. I did use the Operation Reset storyline and one of the players had a CIA operative and I had pre-written some background linking his reason for being there with Reset. However I did juggle things about just to make things more interesting and took a few liberties with the 'Randy' npc's survivability and houdini like abilities so as he became a thorn in the side of the players. The hate of the players of such a betrayer makes a good arch-enemy. I agree it is a little too 'scripted' a storyline - depends on your group - but we had a lot of fun. They were more keen to nail Randy than their actual real goal.
I do tend to let the players do what they want and let the plots and storylines develop from there with the actual scenario as the spine. Krakow for me, in this regard, is more of a base of Ops with a hotbed of rumour/contacts and r+r for my group atm.
As for the original question - I guess you can change the electronics/plans to whatever you feel comfortable with. My group are now in Warsaw causing havoc itching for a way to get back to the UK...more headaches for me
