In terms of commlinks, in 4th they're a bit funky and if you're using unwired there are a few extra bits to consider.
First, you need System and Response to be high, as these cap the number and the rating of programs you can run, which in turn limits your dicepool for certain things.
You can raise these commlink stats to 6 across the board with unwired rules and a lot of cash, but tbh, you're probably fine just getting everything to 5's.
Minimum programs you need (off the top of my head, im a bit rusty with 4th too!):
-Analyse (scans for intrusions and alerts you)
-Browse/Edit (they're cheap, so why not)
-Command (this lets you remotely pilot in AR)
-Encryption (keeps your comms channel secure)
Advanced programs that are handy to have:
-Biofeedback filter (helps soak biofeedback damage if you get shot up in VR)
-Stealth (keeps you off the radar if people are looking for you, good for recon drones you want to keep quiet)
-Track (useful for locating enemy deckers/riggers)
-Decrypt (useful for decrypting enemy rigger's network chatter)
-Spoof (good for causing low-level mayhem against unpiloted drones iirc)
-Agent/Intrusion Countermeasures (IC) loaded with attack+armour software (fights deckers that crack your network for you)
erm... im sure there are more but my 4e memory fails me....
You can spec up the software with customisations, the one you want most of is optimisation to let you take a rating 6 program and run it on a rating 5 commlink.
Crashguard is nice on stuff like Analyse but only useful if your GM is really into matrix stuff (many aren't)
Some hardware options are good on your link too, the optimisation module, hot sim module, sim boosters and such all help in various ways, as does the non-standard wireless link.
Be careful though as you can end up with a 70k commlink in your pocket and you really don't want that breaking or getting lost lol!
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Skills;
Basically all your pilot skills are necessary apart from aerospace (unless actually going to space lol). They work whether you drive/fly/sail manually (in the flesh), remotely (through AR/VR) or jump in (become the drone/car/boat by linking your brain to its onboard computer). If you just send instructions to drones and have their pilot software figure it out, you don't really need any pilot skills, but you're putting an awful lot of faith in the software at that point and it isn't very clever.
If you don't have enough skill points to get a decent repair dicepool for your main vehicle categories, take a high level mechanic contact who can then do repairs for you.
Computer and E-War skills are necessary, so don't skimp. Hardware is decent for repairing damaged electronics like commlinks too.
You'd mentioned staying out of the matrix if you can, this is possible in 4th for a vehicle rigger, you can connect via skinlink (uses the body's bioelectric field to put signal between devices in proximity to skin) or by jacking a cable from your head to the car/bike/plane's computer directly or via a commlink with its wifi turned off.
It won't work for drones though as they'll be too far away.
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Drones;
Some tips for modifying them:
-Armour, as much as you can get
-Gun, get one that accepts belt feed or mod it to accept 100 round drums. You dont want the barrel running dry!! stick a smartgun on it too.
-Sensors, upgrade the shit out of them. you want flare comp/low light/smartlink/image link etc on your cameras and full audio suite on the microphones depending on what role your drone is for.
-Pilot, if using its pilot software autonomously, you'll need to upgrade this as its pretty stupid on most basic model drones.
-Have a mix of combat and recon drones and expect to lose them/get them shot up regularly.
Vehicles;
-Run flat tires on everything
-Morphing plates on everything
-Spoof chips on everything
-Road strip ejector/oil slick sprayer is well worth it in a chase
-Guns, only ever in concealed/turret mounts. don't miss the meet because the coppers pulled you over for having a .50cal on the roof of your car.
-Chameleon coating is a godsend and can make a delivery/utility van into a great stakeout/infil vehicle or can help lose a tail in a chase.
-Have a van with plenty of space if taking bigger drones, sports car for the smash 'n' grab jobs and bike for pursuits/tailing.
-Rigger interface goes on everything you're gonna jump into
-Might need to upgrade system/response if you decide not to go down the commlink route and cable in directly
-Armour is a decent option
-Sensors, as above, pimp the shit out of them.
-Turbos, speed + accel boosts might come in handy but make sure your GM is actually using the RAW before you invest as they're not cheap and won't help if he's handwaiving chases.
You need to have a decent signal rating on drones and vehicles you're going to pilot remotely too, so upgrade that as necessary.