So, anyone up for actually being constructive, rather than putting down and insulting the new guy? I wasn't looking for affirmation of my house rules, and was honestly more interested in advice with the setting/plot.
I hope you have found my input constructive virgil, I don't think I've put you down or insulted you, even when you became combative. And I know it seems everyone is just being dicks when all you're hearing is "you're doing it wrong", but truly the vast majority of input has just been long-time players and GMs attempting to guide you to what they have found to work for a rewarding and fun gaming experience.
The point of gaming should be the RP and the story, the rules are just the framework. Even if the frame doesn't meet end-to-end in some places, it's easy enough to bridge the gaps (adjust target numbers, adjust die pools, adjust whatever - on the fly) so that it makes a good story. You don't need to build a new frame.
My constructive advice:
1. Give Karmagen a try, do the 750 Karma) buy (375 limit to Attributes), plus my formerly mentioned BP Cost = Karma Cost for Metahumanity. If you want to free up a few additional Karma for skills for you players, give them CHAx2 free Karma for Contacts and INT+LOGx4 free Karma for Knowledges. This is actually my favorite way to do Karmagen - though I've never found a GM (yet) who would do it. If you really feel you need to help out Magicians/Adepts (in addition to using Ways and Optional Adept Geasa rules), take MAG out of the 375 Attribute limit.
2. Don't take the Matrix too seriously - which is to say, don't try and take make it as complex as it really should be. You can easily bog down a run, leaving your non-hackers staring at their phones. I'm not familiar with Ends, so I don't know what it does, but IMHO - extract the most salient concepts/programs and use them, water-down the rest, and just strike a balance between a) keep things moving with as few checks as possible as is necessary to b) challenge your Hacker appropriately and c) represent the complexity/difficulty of the system - with a heavy weighting towards keeping things moving.
3. You said your players have played 3rd, so maybe this won't be an issue, but don't be too much of a hard-ass in the beginning - do make their actions (i.e. stupidity) have consequences, but go easy at the outset. The "Big-Brother is Everywhere" thing is where me and my group struggled at the beginning - covering our asses.
4. It's a little cliche to go with the "No Run is as simple as it seems." approach or the back-stabbing Johnson, and while they're both good tools - and should be employed - don't over do it. Some runs should be as straightforward as they seem. But (with advice 3 in mind) then what are the unexpected consequences? Who were those bulbs actually meant for? What is the client doing with the bulbs, and could it come back to bite the players later on? Who's gonna be pissed and looking for the guys that took 'em? What else did they fence that can be used to track them? Have it come down through the grape-vine. Use contacts as integral characters in your story. It's unfortunate when they're just used as proxy checks for acquiring stuff or finding out stuff or mending wounds, etc., in the best Cyber-punk - the "Contacts" are characters you care about and your players should care their Contacts (appropriate to their Loyalty

). Make their Lifestyles a living part of the story, the Neighborhood and Security are given ratings for a reason. Make the story come to them, if they living in a crappy neighborhood (or even if a nice one) and have lax security, thugs see them come and go with fly gear (high-postin', as they say), maybe the get broken into while they're gone and have their stashes stolen - having them get it back is the fun part.
5. Have fun, don't get hung up on the rules.