I just replaced this controller and I still have the book. it says the "ISA 300/400 series" on the booklet and I had the 304. the only difference is the 400 series allows for an optional pump start relay for well water source and 2 different programs. I think you probably were looking at the same book that came with your timer. the "system on" is the same as "auto run". You can check your programmed input from the "preprogrammed schedules" selection on the dial by using the arrows to cycle through the settings but you can't make any changes to the schedule from that position. I had a lot of problems programming this timer, it's not self explanatory, at least not to me. When you select the pre programmed schedule you want, you have to lock it in by pressing the last button with the round black dot. then the square around the letter or number of the scheduled program you chose will be solid instead of flashing. if you don't need to modify the preprogrammed schedule, once you lock it in just turn the dial to system on and that's it. you have to leave the dial at "system on" or it will not run the program. pay attention to the small words at the top and bottom of the screen. it's easy to confuse the start time numbers with the station numbers as there are 3 start times per day available, so if you are entering the start time and you enter the same time 3 times thinking you are entering for 1,2 and 3, the system will start at that time and run 3 complete cycles. When you run the system manually, do the zones run for the length of time they are programmed to run?
for me the last straw was the timer tripping the gfi outlet. took me a while to figure out why the system came on one day but not the next til I realized (read) the screen message. the screen looked like always, date/time and station etc but there was a message "ac off" on the screen also, not blank or flashing like the book says. the power was lost so it was only functioning on the battery which saves the setup info but will not run the system.
So I bought a new timer, much easier to use. And it also trips the gfi ! so now I have a much bigger problem apparently. I still have the book for my rainbird 304 if you need any more info, but I'm pretty sure it's the same book you found on the internet. the picture on the front is of the 408, but the book says it's for the 300/400 series. the phone number for technical support is 1-800-247-3782
good luck.

If its running manually but not automatically, check the power to the box. You might not be getting enough power to run auto program, which takes a lot more than the manual.

I had the exact same problem as "Ron1812". Inherited the 304 sprinklers and had no manual. Explanation from "newtothistoo" was brilliant! Very clear and well written. Got my system working! Only problem was there was no "last button with the round black dot" so I just pushed advance/enter to get the schedule to stop flashing.

I found the "Select Pre-Programmed Schedules" to be confusing. As near as I can tell there are 4 "pre-set" schedules and then a fifth one that you can program using the 3 "custom schedule" stops on the bottom of the rotatable switch - in the "red zone".