I have a 1998 Sequoia Spa. I have two motors, one is 2 speed and one is single speed. I have a leak in the 2-speek motor where the shaft goes into the wet end. What do you think I need to replace? It is also making a whining noise.

Thank you

The whining noise you hear is from the front bearing of the motor. Here's a quick step by step followed by a parts list:

Remove motor and pump assembly
Remove cover of pump (wet end)
Attempt to remove the impeller located in the wet end (usually breaks)
Remove the 4 through-bolts from the back of the motor
Separate the wet end from the motor
Remove the front bell housing from the motor
Polish motor shaft with fine emery cloth
Remove the bearing

Install new bearing
Reattach motor bell housing
Reattach the wet end rear housing, attach with motor through-bolts
Place new seal on impeller (observe proper direction)
Attach impeller to motor shaft visible in wet end
Inspect and replace (if necessary) the seal for the wet end cover
Reattach the wet end cover

Parts you may need are:
Impeller (as this can be very difficult to remove, usually breaks)
Pump seal (or shaft seal as some call it)
Bearing (due to water entry from failed pump seal)
Wet end (or pump) o-ring gasket

It can be quite an involved job to rebuild these, so many people simply just replace as a whole unit with a similar or same assembly.

Would I need to replace the motor and pump assembly or just the pump assembly?

I have a Franklin 4HP motor. What would be an alternative to this motor? What would be an alternative to the wet end and motor as a whole?

You can get the wet end and/or motor separate, or as a whole assembly, from many different suppliers. It is usually best to visually match up the wet end (or if you can read the manufacturer, get the same brand, i.e. waterway, vico, etc)

The important things to consider are:

Hp, keep it the same
Center suction port size (2 or 2 1/2")
Discharge port location (center, offset...also known as side discharge)
fitting type (ball or standard)

If you want to just get the wet end, and repair your motor bearing, that is perfectly fine as well. I would suggest, if you go that route, you try to repair your motor before ordering parts, just in case you determine you would be better off with a new motor also. It's usually cheaper to get the motor and wet end as an assembly.

What does the motor bearing look like? Can I order it from SpaPartsNet.com?

The bearing is just a normal simple sealed bearing, available pretty much anywhere locally where bearings are sold. You will need to get the numbers off the old bearing, so you will need to remove the bearing first.