I have an old intermatic air swith control box that is brown in color, and the wiring diagram has come off the switch still works how ever I'm trying to hook it back up going trough a timer and not having much luck. Any suggestions?

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99% chance the Timer wires are reversed ... and line from breaker and line to pump are reversed. Or remotely possibly the circuit is 240V, and somebody changed clock motor on old T101 from WG1570 to WG1573, converting old T101 into T102...
http://waterheatertimer.org/How-to-troubleshoot-Intermatic-timer.html
http://waterheatertimer.org/How-to-wire-T104-Intermatic-timer.html#T101
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your mirror control switch has 9 wires.,your drivers door mirror has 5 wires color coded .from your mirror control switch to your drivers siide mirror / 0.5 black .0.5 brown. 0.5 brown. 0.5 black. 0.5 black.
your passenger mirror wires are 0.5 blue/black .0.5 blue/grey. 0.5 blue/white. the passenger mirror has a ground cable 0.5 brown.
the passenger mirror wire 0.5 green/white connects to a 5amp fuse/F25 onto F31 5amp to a wire 0.75 green/yellow.back to the mirror control switch.

You might need new trippers?
Problem is not fully clear.
Can't tell what is new, and what is not working. Add a comment.

You have a new timer with same problem as old timer.
And you have a new control box and switch.
At your new house.
You have RC2343PT air switch, likely with PB913N84 24-hour timer module with manual override knob.
http://waterheatertimer.org/images/Intermatic RC2343PT.jpg
http://waterheatertimer.org/pdf/Intermatic-PB800-PB900-timers.pdf
http://www.poolandspacontrols.com/~/media/Files/PoolAndSpaControls/Products/Instructions/RC2403RT.ashx

The RC2343PT air switch operates a pool-n-spa blower switch.
Pool and spa blower successfully turns on-and-off with circuit breaker.

Did you install a new PB913N84 timer module?
Are both ON-and-OFF trippers present? Are the 107TN222 and 107TN221 on-off trippers worn down and need replacement?
Does the timer dial rotate and keep good time?
What happens when you manually rotate the timer dial clockwise two rotations? Does the blower turn on-and-off?
Have you checked wiring terminals for signs of loose or burned connections?

Add a comment with more information for possible additional help.

No. I don't have a wiring schematic without knowing what voltage you are using, specifically what Intermatic timer you have, specifically what wires you have coming from breaker box, what wires are on the pump, and what pump rating plate says, what the wiring diagram shows on side of pump, whether you are wiring a 2-speed pump to a single-speed timer, specifically what is the polaris timer clock, and why this pump needs two timers if that's what you mean.
Add a comment with specific information so electrician is not guessing.
http://www.poolcenter.com/polaris-booster-install-OM.pdf

Open following link for 240Volt T104 timer wiring diagram.
http://waterheatertimer.org/How-to-wire-T104-Intermatic-timer.html

Photocells are always 3-wire. The photocell switch has to be powered continuously, while power going to the load is turned on only when switch turns on.
Intermatic K1100 pages says: "three 6 in. color-coded leads"
http://www.intermatic.com/products/ec%204%20layer/photo%20controls/k1100%20k1200%20series%20relay%20type/k1100%20and%20k1200%20series%20relay%20type.aspx

Same 3-wires are required when photocell controls 120Volt or 240volt.
Open following links for some diagrams and information:
http://waterheatertimer.org/Intermatic-trippers-and-parts.html#photo

1) T101P201 timer does not have a separate manual yet
http://www.poolandspacontrols.com/products/mechanical%20time%20switches/pool%20and%20spa%20time%20switches.aspx

2) However typical T101P201 timer is ordinary T101 timing mechanism inside Nema 3R beige-colored outdoor plastic enclosure, with additional fireman's switch.
Wiring for T101 shows on following link, and shows on door of timer enclosure:
Check that your timer terminals match illustrations because many timers can fit inside Intermatic enclosures.
http://waterheatertimer.org/How-to-wire-T104-Intermatic-timer.html#T101

3) Fireman switch wiring:
T101P201 has a fireman's switch that wires directly to the pool heater thermostat.
http://waterheatertimer.org/pdf/Intermatic-Firemans-switch-156T4042A.pdf
If you are not using the timer for pool heater, or if heater does not have connection for fireman's switch, then do not connect fireman switch wires, and just tape them out of the way.

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Need more information.
Project is not clearly defined.
Add a comment with clear description of each wire and what Load is being controlled.
Why are you using a 4-way switch? Are you controlling 240Volt circuit?

Photoelectric switch usually has red, black, white wires, and usually replaces a single pole switch but can also be used to control 240Volt circuit in some wiring diagrams.
http://waterheatertimer.org/images/Wire-photo-eye-125.jpg

4-way switch has 4 screw terminals and is generally not used to replace a single-pole photoelectric eye, but can be used to control 240Volt circuit in some wiring diagrams, so I'm not sure what you are doing.
http://waterheatertimer.org/images/Typical-3-Way-switches-450.jpg

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You posted under Intermatic 240Volt T-1906 box-type timer:
Look at model number on inside of timer door.
If this is not your timer, then link below doesn't apply.

Wiring diagram appears on following link:
http://waterheatertimer.org/How-to-wire-T1906-Intermatic-timer.html

It seems unlikely you have expensive 240Volt box timer for aquarium light.
So add a comment with clear description of your timer/switch.

If you have wall switch instead of timer, please describe the device, and screw colors on device, and wire colors inside box.

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For a price, expert speaks with you over phone while you work on your do-it-yourself project.
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your mirror control switch has 9 wires.,your drivers door mirror has 5 wires color coded .from your mirror control switch to your drivers siide mirror / 0.5 black .0.5 brown. 0.5 brown. 0.5 black. 0.5 black.
your passenger mirror wires are 0.5 blue/black .0.5 blue/grey. 0.5 blue/white. the passenger mirror has a ground cable 0.5 brown.
the passenger mirror wire 0.5 green/white connects to a 5amp fuse/F25 onto F31 5amp to a wire 0.75 green/yellow.back to the mirror control switch.