My question is when a recipe calls for a specific time to rest, when does that timer start and stop? What about the time in between when raising the temperature from 122 up to 148 then to 158 (hypothetical but typical mash rests - I'm trying to ask this question style-agnostic) are you running the timer during this 'step up' part as well?
I typically run my timer when I get to the target temperature. However, in my mind it would depend upon how long it takes you to get from step to step. When I step mash, I will do it with either infusions, which means it takes no time to get to the next step, or by decoction, which means it takes a long time to get there. Remember that the enzymes work over a pretty broad range so if it takes you a long time from one step to another, they are actually converting starches along the way.
Just as a background on my mash tun equipment, I use a keggle w/ false bottom and am considering using a pump to circulate the mash while heating up to the next temp. I also have a concern here about the heat melting the tubing connected to the valve at the bottom.
This would depend upon what kind of tubing you are using. A figure I have in my head, which very well could be wrong, is something like 150 F for standard vinyl tubing. You can easily get high temperature tubing such as http://www.northernbrewer.com/brewing/3-8-hose-hi-temp-vinyl-safe-to-212-f.html
Also, when heating to the next step and you are beginning to approach your target temp, do you throttle back the heat so as not to overshoot the target?
I don't run a RIMS or HERMs system, but what you are describing is what is known as proportional control and is generally a simple and good technique to use when controlling something.