Wow, that's quite a lot of questions. I'll try to answer as many as I can. Strangely enough, I've already considered the answer to most of them.
I'm aware that the spirits need an action to materialize. In combat, this may make them vulnerable for an instant. Out of combat, though, it might still be possible for a suddenly-manifesting spirit to surprise you. Thus, an initiative roll. It's a GMs call, though. What I should have done is asked for things to remain in combat time, then had the spirits manifest on their third action phase. Then, again, it would have been down to pre-rolled initiative values on the next Action Turn. I didn't think I'd need to do this, though, due to my first point, above. As I mentioned though, it doesn't matter. I didn't actually care.
A magical jammer may still be inhibited by a Faraday cage or wifi-inhibiting paint.
Note that a rating 5 jammer would also have normally cut off communication between Raven, the group, and the drones. Only Raven himself has a R6 signal. This problem would have been rapidly solved, however, as Raven distributes R6 ECCM (optimized) to the group, and the drones start up their own copy. If for whatever reason a Faraday cage doesn't work, this same strategy can be used to overcome the magic ECM, by distributing pirated copies of this software to anyone who needs it, and running a copy on the satellite dishes.
You are asking someone with no actual knowledge of how to investigate magic how he's going to investigate magic. I can't do that. Raven is the expert, only he knows how to do something like that. All I can do is tell you some of the options. Magic Theory should help, as it is more than just a list of "these are the kinds of things you know magic can do". Rather, it is a fundamental (and genius-level) understanding of the fundamentals of how magic works. Beyond, that, it's up to you. What does raven think it is necessary to do? I'm not going to pixelbitch here. I've already named one particularly dramatic way of finding out, a groupwide metaplanar quest. It's up to you, though.
It sounds like this "commcode" is magic. I don't have any ability to deal with that, there just aren't any rules in Shadowrun or the real world to explain how something like that could possibly work.
The rigger cocoon is attached to the rear of the drone, exactly as you see in the Tachikoma (please do watch the linked video if you are not already familiar with GitS).
The tracked and hover modes have not been removed, they are in fact the primary mode of locomotion. Legs fold down for use only when needed.
I am aware that I am overmodding the drone, by exactly 2 slots. I have paid the standard double cost for those two slots. I have not sought GM permission because 1) We have 3 and climbing GMs, and it's already a cluster****. 2) We're already playing ridiculously fast and loose with rules, with binding F12 sprits when the rules specifically mention that spirits use Edge to resist summoning and binding when they are much more powerful than the summoner (p. 95, Street Magic) and 3) If someone else gets a ridiculous toy, I am too. However, feel free to ban the drone when you are GMing. It's not needed when Walker isn't in the group anyway.
I did not take "Improved sensor array" mod. I just paid to upgrade the existing sensors to R6 plus extra goodies. The Hussar also already comes with a reinforced turret mount.
I do not use the heavy autocannon because a gun that big would be larger than the entire drone: it's a main tank cannon.
I'm no more worried about heat from the gun affecting the grenade launcher than I would be worried about the heat from the gun on an Ares Alpha detonating the grenades in the underbarrel clip.
I'll stick with just warding Raven's apartment, in that case. I may later also ward the Bunker, but not yet.
