[swaghauler]

I like your espionage ideas. Try to get a copy of Mercenaries, Spies, & Private Eyes. It has a good section in it on designing "mystery" sessions. I have been developing a MERC based hybrid game I call Contingency Force based on my Security and LE experiences. In a nutshell, my players will be PMCs forced to deal with a variety of situations in the third world. Based on my experiences with companies like Blackwater/Xe, GlobalTech, and Saris. They will have an operational budget and have to answer to superiors about their actions. Since the world is still intact, they may get a reputation or make enemies who haunt them. I'm basing it mostly in Africa (because I served there) but they may end up anywhere in the world where "guns for hire" are needed (there are several opportunities in Eastern Europe, South America and Asia right now). It will be part military and part espionage game.
I have blended several rules to allow for CQB which may help you.

I changed my damage rules to increase weapon damage and make injury slightly greater. I use the older D10 system mixed with the newer D20 system. for damage dice I use D10's instead of D6's. This increases pistol damages to where it almost merits carrying them. But players must be more careful as a result.
Hit capacities get seriously lowered. I use a system incorporating CON, WILL (an added stat), STR, and Stature (from V1 rules) but you could just use CON. Hit Capacities are: Head (CON), Chest (CONx3), Abdomen (CONx2), Arms (CONx2), Legs (CONx3). This is for your Slight damage threshold. I use 5 Damage Thresholds (with appropriate penalties) My Damage Thresholds are Slight, Moderate, Serious, Critical, and Deadly wounds. Death occurs in CON+WILL minutes from exceeding Deadly wound threshold. For NCPs, I would just use CONx3. Limb hits would do 1/2 damage, Head hits would do double damage. Just make note that this system increases player mortality. A typical player will have 25 Hp in the head and a 9mm FMJ can do 20 points of damage under my system (hollow points would do +1 per die more).
I throw out the auto fire of weapons rule and just throw a number of D10's (you could use D20's) equal to the burst size. The difficulty is one level worse than firing SA. Recoil rules stay the same from version 2.2. I found out an interesting fact shooting competitively for several years. Full auto weapons with realistic rates of fire (where the shooter is going for accuracy) are easy to mirror in Twilight. Just divide the weapon's cyclic rate by 100 and round down. An AK with a cyclic rate of 600 RPM would have a ROF of 6. This rate of fire will result in slightly lower or higher rates than listed in Twilight. I does add variety to your weapons without complicating things too much.
To get a detailed action sequence that's still playable; I hijacked 2013's "tick" system. My "Initiative system" is determined by a character's WILL (I added this trait) and AGL and is ranked from 1 to 10. You then roll 1D10, generating a modified (by Damage, Coolness, or Surprise) score from 0 (min) to 20 (max). Each "tick" is 1/4 of a second.
The players state their actions for a round from highest Initiative to lowest. The actions are assigned a "point/tick cost" based on how long they would take in real life. If drawing a pistol takes one second, that is 4 "ticks." This allows for dynamic actions to be resolved in a realistic order (ie. is that knife attack faster than your shot?).
I also like 2013's Coolness Under Fire rules so I hijacked them too.

Good luck with your game. The game I'm working on now is my continuation of a project I started way back in 90' while in college (that was interrupted by my military and LE careers). I went to Allegheny College before I finished my degree at Mercyhurst (Criminal Justice). We might have gamed together.