1. Are there any modifications to the standard way of typing that can make it even better (other than ergonomic keyboards or physical changes to the keys)?
Normal mechanical keyboards, or better, a Kinesis mechanical keyboard.

2. Is there any benefit to retaining my ability in qwerty?
The benefit is too small compared to the maintenance cost.

3. And if you are typing a long series of characters in uppercase, do you repeatedly switch from left to right shift and back as the actively typing hand changes from right to left and back? It feels a bit awkward to me.
I use AutoHotKey so by using a script I can turn on/off Capslock when typing in Colemak (Shift-Capslock or Control-Capslock toggle Capslock).

4. Also, how do you type the right shift without moving your wrist or feeling awkward?
The awkward feel will be diminished after two weeks of practising.

5.And should I change to Colemak on my phone as well?
Not necessary, since on the phone we use only two fingers to hunt and peck.

6.Thanks!
You are welcome!

Regarding the shifting, when I started to touch type, I forced myself to alternate, which was a bit of a challenge.  I got used to it though.  Stick with it, you can deviate to whatever feels comfortable later.

As has been said, if you have more than a few capital letters, reach for the capslock.  Or you could even try sticky keys (much nicer...).  I struggle to hold and depress the shift lightly -  I feel it's a bit of an assault on my fingers.

I think I actually find the left shift more of an issue on my laptop in terms of twisting.  Then again it's a shorter key than the one on the right, which might not help.

As for other modifications and possibilities, look at my signature post – especially the color-coded fingerings (and note that I use an optional WideAngle mod for even better ergonomic benefit) and the Extend layer.

These aren't implemented on the Mac that I know of (although I think there's a Wide modded Colemak layout out there somewhere) but it should give you a few ideas of what you can do! :)

I've started my switch to Colemak on 28th March 2013, awkwardness starts diminishing after 10 days.

I trained using gtypist (ugly, text mode, unix software). I went through Colemak tutorial series, I also generated my own drills. I used word frequency data and my own script.

My current problem is: I can type with 97+ percent accuracy on typeracer, but only if I limit myself to ~30WPM, if I try to type any faster my error rate jumps sky high. My accuracy also sucks, when I do software development, or compose a message.
Do you have similar experience? How do you cope with it?

Very true in my experience.

My favorite qwerty-like keyboard for phones is probably dvorak, since its high hand-alternation rate translates to high thumb-alternation rate.  That should already be available on cydia (though honestly, you need an android - for some stupid reason, since keyboards are software and ought to be infinitely flexible regardless of platform - if you want to get at the real touchscreen-optimized keyboards like messagease).

I think that what he meant was that MessagEase cannot replace the default keyboard in iOS. MessagEase is only available as a standalone app. Even Cydia doesn't have it. The best alternative for faster typing is Touchpal keyboard which is available in Cydia and can replace the standard keyboard, but it does not support the Colemak keyboard layout.

Also, should I aim for a low viscosity in Amphetype?

Sorry for the convoluted English! You're right, you need to type in the messagease app then copy and paste into other apps. It doesn't replace the keyboard in all apps.

My only problem is that I cannot get my version of Android to change the "unlock screen" keyboard to MessagEase.  Other than that--I'm using MessagEase in every "app" I have on my phone.  Apparently newer versions of Android provide the ability to change this, but I have a lower-end phone (LG Optimus V) that runs 2.3/Gingerbread.

@caspersong, thanks for clarifying.  Seems that Android is at least going in the right direction.

I showed MessageEase to an iPhone user, he took one look at it, said it was ugly and moved along!

When I type I usually either think too fast to read too fast and that results in me typing the next bit even though I haven't finished typing the word I currently type. I also tend to mix up the order of the letters I type. Does anyone have any advice for me on this to stop these kind of issues?
Type slowly to get accuracy at least 98%. Then try to increase speed bit by bit. If your accuracy falls below 98%, slow down to a comfortable pace.

Besides, is low viscosity good on Amphetype?
Yes, it means you type in rhythms.

I agree, viscosity is inapt. I still am not sure I understand what it means.