TMI!
We need to understand exactly what is happening and when.
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Held down SHIFT key after the chime. No Apple logo.
Just a gray screen again!
I've also disconnected my Seagate EHD.
"disconnected" when? Before the Safe Mode startup? During the "grey screen"?
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WAIT! Apple logo just showed up.
After disconnecting the EHD? How long after the Startup process?
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It's taking a while to boot up. Hmmm. What does that mean?
Did you read the info on Apples instruction page?
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It rebooted, but icon for EHD#1 was missing.
Assuming it was now connected, again. Don't ask us to 'assume', please tell us specifically what you do between each step/action.
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So I restarted. Gray screen again!
Safe Mode or 'normal? There is always a gray screen on start up. The duration depends on the speed of the computer, the drive and how well it's sectors are arranged.
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Waited 4-5 minutes and a Gray Folder with "?" showed up.
That usually means there is no usable System on the drive the Mac is trying to start up with.
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That disappeared and now everything is showing on my desktop again...
However, since it finally does complete the Start up, it's likely that the drive is starting to die or that there are many bad sectors on it, especially in the main directory. It may also mean that the booting sectors are completely out of order.
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...EXCEPT EHD#1.
Again, I'm assuming it was (by now) reconnected? We (I) simply cannot trouble-shoot by "assuming" things. Computers just don't operate like that, only humans.
First, check System Prefs->Startup Disk and make sure your internal, builtin drive is selected. If it is not, it will 1) waste a lot of time searching for the non-connected disk, 2) Waste time looking for a bootable System on any external disk that may be connected. Eventually, it will give up and look at the internal dick and the Startup process will finally begin.
I suggest you discontinue trying to use the external drives until you can get the internal drive working properly and consistently. If you have a stop watch, use it to keep track of what is happening when. Otherwise, an analog clock/watch can help. If nothing else, an egg timer (sand or mechanical) might help. There's one other timing method, but Sun dials are so rare now...
One (detailed) step at a time...