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The Apex II is a very good upgrade.  I have one on my A5.  Forget doing lob shots with it but instead tune it for accuracy.  You may want to clean the ramp with some Armour All wipes before you shoot from it.  What are you running for gas?  CO2 or HPA?

The R/T tends to run better off of CO2 in my experience, especially when using other upgrades that tap the blow-back exhaust for their operation (eg, cyclone feeder). Mind you, that can be countered with larger lp lines and banjo fittings for higher flow at lower pressure, but it's still better to run CO2 if you're wanting to upgrade a bit at a time.

As for the vert adapter and expansion chamber, just about anything is going to work well. Some expansion chambers have more baffles in them to reduce the possibility of liquid getting sucked into the valve than others do, but with a Tippmann, it's not as much of an issue since the CVX vale is so hearty that it can handle liquid CO2 just fine.

Depends on what kind of paint you're shooting. You want the paintballs to match the bore size as much as possible to increase accuracy. Most paint runs on the smaller side these days, so I'd lean more towards the .687 myself, but if you're using larger sized, lower-quality paint, then it might be better to go bigger. Grab some rounds from the paint you think you'll use most and put them in some calipers. Average out the diameter and go with the closest bore size to that.

You might be interested in buying new cyclone internals. I bought Chinese knockoffs of TechT stuff. I knew it wasn't working right, then the older OE ratchet disintegrated when I replaced it.