Need wiring diagram for Hayward dual Super 2 speed pump. Old unit had 3 wires and new unit has 5 wires.

Not sure if you will find such a diagram...
New installation?
Do the pumps have their own breaker?
Is your Super II pump a 2 speed?
What is the Thermostat for? Do you have a heater that you are trying to connect, so that the pump will come on when there is a demand for heat? Not really sure what the T-stat is mentioned for here?
You still only need to have 2 timers if I'm not missing something?
The T-106 will be for the Super II pump (presuming it is a 2 speed version) It will turn hi speed, on & off. or switch between them rather. I think I see why you may be inferring about a 3rd timer? You don't want to have pump running on "Low" speed continually. If so, Then you will need a 3rd timer (T-104) to provide power as Line to the T-106. The other T-104 will be for the booster pump for your cleaner.
The power for the Super II pump from the breaker will go to the 1st T-104 as "Line". Then from the Load portion of that timer, you will wire into the Line portion of the T-106. Following the instructions from the diagram at this website address for a PDF document:
http://www.intermatic.com/~/media/Intermatic/Documentation/Time%20Switches/Mechanical%20Time%20Switches/24%20Hour/T100%20Series/T106R%20Instructions.ashx
you will complete the wiring to the Super II pump via the "Load" side of the T-106
The 2nd T-104 (pool sweep pump) will be wired: from the breaker to the "Line" portion of the timer. From the Load portion of the timer, you wire to the booster pump.

Good Luck

Fixya does not sell Intermatic P1353 timer. We answer questions for do-it-yourselfers like yourself.
Open following link for Intermatic P1353 manuals with wiring and programming diagrams.
http://waterheatertimer.org/Intermatic-trippers-and-parts.html#P1353

1) It is very likely that pump wires will change over color-for-color, but I am electrician and would never do that because I would not want to burn out my new motor without poking around first. I would look at manual for old motor and compare with manual for new motor. I would certainly read the new manual and compare where wires are connected to timer.

2) As a general rule with P1353 timer, High speed connects to terminal 4. Low speed connects to terminal 6. The remaining wire connects to terminal 3 with a jumper wire to terminal 5.

3) This information applies only if you are replacing a 2-speed pump, and timer was wired by diagrams shown in the manual, and timer is correctly programmed for MODE2 2-speed pump.

4) You can add a comment for more free help. I will answer back. I know this timer front and back, it is complicated for novice. And you should remember that I do not know what is inside your pump manual unless you tell me, and I do not read minds.

5) You can also pay for fixya expert to work with you while you work on pump.

It will not matter where you put the hot and neautral as long as one goes on line 1 and the other on line 2. Just be sure to reset the voltage indicator to read the 115V like before and your all set.

What specifically are you looking for (beside the fact you asked for a diagram)?

It should be setup for 220 Volts ... the only thing inside is a start cap.

Can you tell me more? I maintain 5 2 and 1 1.5 hp such pumps.

Is one screw silver and one brass? Or are they both silver or both brass?

Recheck your wire connection on the motor. You likely put both your line wires on the same terminal. If not, try finding a local warranty center for a repair or replacement... http://www.haywardnet.com/locator/