First up, an old issue that you may well not consider to be a bug - At the start of the game, you still have to go to The Cage and get kicked out to get the "Tickets" keyword. In the actual US SNES version (the final version, I have know idea how it is in the beta), the guy you gave the tea to would give you the "tickets" keyword, which you could then use to get the Grinder and Lone Star keywords from him. In any case, this kinda breaks story continuity, since it requires Jake to go to The Cage before he should know he needs to. Note that I did read in your changelog that you added a hint to one of the NPCs in the area about going to The Cage, but I never found it, tho I didn't look very hard. Until I see how this is done (I might start a new game just to check), I'll hold judgement on that solution (my first thought about it is that it's a kludge).

Now for the rest...Balance seems alright now through much of the game, except for one thing - the Ruger Warhawk pistol. For 300 nuyen, you get a 16-damage weapon with unlimited ammo (anyone who uses pistols without getting auto-reload is nuts). The only weapons in the whole game with higher damage are sniper rifles (one of the shotguns matches it, but they don't beat it and they have very limited ammo per reload). Not only that, but one normal rifle offers armor penetration - and its damage is enough lower than the highest rifle (not to mention the Ruger) to make it not worth the nuyen. Granted, you don't get to use double-tap with the Ruger (which is why I took up rifles later - crits just became too valuable, and the damage is just too low on non-revolver pistols), but that one gun will still tear up the game through Drake Tower, including the Arena. My suggestion? Increase the price on this baby (it should be one of the more expensive guns at the first shop) and/or move it to the Dark Blade shop.

Now for the 2 new areas since my last playthrough - Drake Tower and Drake Volcano (yes, I know the Volcano is still under heavy construction, but I was actually able to complete it).

Drake Tower
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Other than some layout problems with some of the floors, this seems fairly well-balanced. I like that you put in a "stealth" option for those who want it, and have a couple of suggestions:

First, make it so that when you click to pick up a disguise it asks you if you want to put it on (and leaves it on the ground if not) - this is for people new to this version who want to just blast their way through like they did in the SNES version, or who otherwise don't want to use the stealth option. Sure you could just say "well don't touch that", but how is someone new to the game supposed to know not to pick up those 2 items?

Second, if this isn't alredy implemented, make it so that if someone gets through a floor with stealth, it "clears" the floor (making it impossible to aggro the guards there, or removing them entirely) and grants Nuyen and Karma equivalent to what you would have gotten for actually killing those guards. This makes it so that people using stealth don't fall behind for the Drake fight and/or Aneki Tower.

Drake Volcano
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First things first - your "first draft" of this place is amazing. Kudos on the layout and the changes.

Balance: For the Karma I had (197 spent, which seems reasonable), this place, for the most part, seems almost too easy. I know you mentioned freeze bugs - I never ran into any, tho I might've just gotten lucky (I did run into a couple of those in other parts of the game tho, and had to reload using the debug menu each time). Most of this can and probably will be solved by putting a few more guards in and/or making more guards appear when the alarms are set off.

That said, there are a couple of specific issues with Sub4:
First, the big wide-open area with all the turrets in it needs to have the turrets not activate until you're in the room, and then have all 4 activate at once (they currently activate one at a time, and are waaaay to easy to blow up singly). The room might need to be made smaller and/or the turrets moved a bit closer to the entrance to accomodate this. The addition of a Troll Decker or 2 in there might also help things since Turrets, by themselves, aren't all that threatening to a well-geared character with decent cyberware (and with gear prices the way they are currently, most characters rolling through there will be).
Second, back in the back of the area (where you go to disable the turrets and/or kill the guys who would be tossing grenades at you while you approce Drake's actual lair), there are 2 Troll Deckers standing next to each other (one is obviously a Janitor, but who cares). When you aggro the first one, the second one (the janitor) will stand there and watch you kill him while doing absolutely nothing. Then, when you step a bit further into the room, the "janitor" will aggro you as well. This fight would be a lot more interesting if they both aggro'd you together. This could be done for other encounters in the Volcano as well.

Finally, a bug with the area - when you talk to the pilot she gives you 3 options: Drake, Volcano, and Docks (keyword-based, ofc). In the SNES version, she responded to Drake and Volcano - and those keywords would take you back and forth between the tower and the volcano. In this version, the Drake keyword is for story, and the Docks keyword is apparently supposed to stand in for the Drake keyword, and take you to the Docks instead of the Tower (which is fine). However, when you travel to the Docks this way, you permanently lose all hired shadowrunners, including Kitsune (they may be re-hirable, but I didn't try, I just rewound to before I finished the tower so that I could hire Frogtongue to take with me into the Volcano). Again, I know this area is new and marked as unplayable (it's not unplayable, trust me, just unfinished), but this bug is a bit troublesome to someone like me who always goes out of his way to get Kitsune to tag along.

Now, an overall suggestion that may help remove some of the old "transition" bugs you seem to have: Remove the ability to just "hire" runners - make it so that all runners, even Kitsune, are "on call" only (To keep the flavor of the SNES game, if you finish the Rat Shaman's with Kitsune in party, she can be called in for free, or better still always comes in when you enter a "hostile" area). I'll be honest: Jake doesn't need runners with him in "town" zones at any point in the game (I never ran into any real "problems" in town). Making it so that entering a "hostile" area gives you the option to bring in runners, and making it so that runners don't appear anywhere else, has the potential to solve quite a few long-standing bugs in the game.

--Arek75