John,
" ... how does one incorporate what seems to be a universal passage of time, from past into future, with variable clock rates?"
One doesn't, if relativity is true. There is no universal time, and "all physics is local."
"Do we construct a complex four dimensional geometry, in which the dynamic present is an illusion, in order to fix the events occurring at different rates into one framework, or do we view the process, what is occurring, as real and the marks as subjective, ie what comes into being and then is erased, ie. going from potential, to actual, to residual?"
You're mixing up incompatible models. A geometric flow differs from a metric measure ("potential to actual;" "residual" is not physical) in that global least action is nonlinear and not simultaneous with local least action. It's an open question of whether a complex system model bridges the local-global distinction (the subject of my ICCS 2007 paper, "Time, change and self-organization").
"As you say, the marks; yesterday, today, tomorrow, etc. are not physically real. What is in the interval, the process occurring, is. So wouldn't we take the process as the constant and the marks as the variable? Therefore it isn't the present that moves, only the marks."
How does a process constitute a constant?
"So I consider the action, the processing of the interval, to be physically real."
But you said the process is a constant. This is equivalent to Zeno's arrow paradox, and motion is impossible, in principle. Do you understand the contradiction?
Tom