What do you mean, "that is a transistor package alright!"? I don't think you realize how many decades I spent building my own circuits and gadgets far before I even was granted two degrees that say I know what I'm talking about by the most selective engineering school in the nation.
Please read my and Ult Dev'r posts more carefully and don't waste our time by not reviewing posts carefully before commenting on them.
Comments on your paper:
1) You switch the collector-emitter current, not the collector current. And it scales as an analog value; it's not switched (first para)
2) Make it clear that you mean "high" or "low" with respect to the collector (or emitter) potential, not digitally high or low
3) Make it clear somewhere that transistors are analog devices that can be used for digital purposes somewhere in the first or second para
4) NOT is not a fundamental gate. You can make a NOT from a NAND with its inputs tied together.
5) As a certified Engineer-in-Training and a dual-degree-holding Electrical Engineer, I'd dispute the statement "How do engineers remember which gate is which? They have a system of symbols.". That's how we represent them, that's not how we remember them.
6) "The symbols shortened the design of a micro-architecture. No longer was it necessary to write out the transistors and resistors that make up the gate." <- I don't think anyone has designed a "microarchitecture" using transistors and resistors. Perhaps "microarchitecture" is not the word you're looking for?
7) The gates->opcodes transition is very abrupt. Make it a little more gradual if possible
8 ) "All of the functions the computer can use are connected to the CPU by physical connections. " You mean all of the "hardware", and make it clear that it's indirect in some cases (cf Southbridge, Northbridge, chipset, controllers, and related concepts).
9) "Well, a clock-speed basically limits the instructions from being sent to fast. The semi-conductor can only oscillate at so fast a frequency, without error. When a person OVERCLOCKS a CPU, it means that they risk errors. The CPU has been rated at a lower clock-speed, so the information is sent slower." This is wrong. The semiconductor (not "semi-conductor") can "oscillate" quickly. However, the time for an electrical signal to get into and then out of a gate is limited by the speed of light and the size of the chip. Multiply that by all the gates that the signal has to travel through in a single cycle, and you get a limiting factor on the clock speed. Modern CPUs do extensive, extensive staging and parallelism to ameliorate this issue.
10) "REGISTERS allow the CPU to do its commands. " Also wrong. Registers store intermediate data used in commands. Your explanation following this statement is correct, however.
11) You don't "stimulate" flip-flops, you trigger them.
General comments: you usually
italicize new concepts as you introduce them rather than CAPITALIZE THEM. Use more formal, less colloquial phrasing.