Well, no response so I'm going to update with what I've found out myself. I've ordered the parts and I'm going to start as soon as I get them. I will be posting pictures as I go.
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1) The pump itself is a 3.5HP Magnetek that says 38 SPL on it. I know that the SPL means 'special' and that it's not going to reach and run at 3.5HP. My question is how do I test this motor works? Can I just connect the red/white and black/white to 110v separately to verify? How do I determine if it's a 2 speed pump? Any way to test the different speeds?
I took the pump to a local hot tub store. I didn't have the pump with me when I had originally posted my questions and a lot of them were answered when I got home. I still don't know about the testing procedure but I do know that it's pretty easy to determine if it's a 2 speed pump.. it said so on the label!

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2) The wet end obviously had some left over water in it and was ruined by expanding ice. How do I know what wet end will fit the motor I have?
I matched up the numbers on the existing wet end and found the exact replacement. My concern before was that the wet end was a 2HP and the motor was a 3HP motor. However, I checked all of the specs on the motor and everything was telling me a 2HP motor.
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3) I am thinking about buying the Smart Touch Digital 1000. Can I cut a hole in the top of the tub to mount the control panel? (See the picture) If so, how do I cut the hole?
I didn't end up going with the Smart Touch Digital 1000, I didn't need that elaborate of a system. However, I did find that, yes, I can cut a hole in the tub to mount the control panel. I'm drilling a starter hole and then cutting the the rest with a sabre saw.
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5) The seals around the jets in the inside of the tub seem to be dry rotted. Can I take them apart and just silicone them? If not, where can I get replacement gaskets/seals?
I'm going to fill the tub up with water first to see if I have any leaks. This one is on hold for now.

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7) Is that a filter on the bottom of the tub or just where the water circulates?
It's the lower drain.