I think I remember having this happen once also. Check the lead from the ESC to the timer. Make sure its on the correct pins on the timer(brown wire to the pin by the letter G and orange lead on the left outermost pin,Hubin timer).
Bob

It sounds like two different problems: the motor running backwards because the ESC to motor wiring got mixed up, and the beeps because the ESC to timer wiring got mixed up, or something broke.  Did you maybe unplug things in a hurry when you got the reverse running?  Could you have plugged them back in wrong?

To fix the motor-backwards issue, you need to reverse any two wires from motor to ESC.

To fix the always-beeping, you need to carefully check that the ESC is plugged in correctly, and that no wires are broken.  If you have any RC gear, you can connect the ESC up to the throttle channel of a receiver and see if it responds correctly to the throttle stick on the transmitter -- if it does, then you know the problem is with the ESC, if it doesn't then things are still up in the air, but point more toward the ESC end than the timer end.

If the ESC works with your RC stuff, then the ESC is not the problem.

Either the timer is somehow messed up, or you're somehow not connecting it correctly.

I'd hook the timer up carefully per the directions, step-by-step (probably after taking the prop off the moto to insure I don't accidentally slit my wrists), and see if it works.  If not, then I'd call or email the seller or the manufacturer (is it a Hubin timer or KR or what?).

The 3-wire servo/ESC/etc connection that's common these days can be connected in reverse and not break the electronics.  So the first thing I'd check is that I don't have it backwards -- but contacting someone who knows that particular bit of electronics first is probably a good idea.

Which timer do you have?

I have had problems when testing an esc with a RC transmitter and then going back to the timer. An esc out of the box will normally look for a 1ms start pulse. The RC unit might set the esc lower or not as low as the timer if you range set the esc with the RC tx , you may be out off range for the timer.

 I have not used that particular timer, but what happens is the esc does not always recognize the low throttle rate set by a RC tx  . I check the output rates using a GWS meter and if the RC tx is at fault I use the meter to range set the esc to match the timer.

One more thing.  It sounds like it worked on the bench, including with the timer.  I had an install fail when bullet connectors touched with barely visible brass showing. Are ure motor bullet connections tight to each other?  If they are tight to each other, try opening them up, if that solves problem then either tape or shrink tube over the bullets.

If signs point to Timer then get a replacement.

What the RC guys call a servo tester is a handy tool for electric.  It plugs into the speed controller in place of the timer.  As mentioned in the previous post it can be used to test and or setup the speed controller.  They are cheep on eBay.  Search on servo tester in the hobby section. Fancy ones cost $30 +, simple ones $5

http://www.ebay.com/itm/3CH-ECS-RC-CCPM-Servo-Consistency-Master-Servo-Tester-Speed-Controller-FKG-/371047954051?pt=Radio_Control_Parts_Accessories&hash=item56642e7683

There is no such thing as an electric 1/2A, only a small electric motor.  A 1/2A is a piston engine with less than .05 cubic inches of swept volume.
 
That being said, maybe your motor is just trying to be a Babe Bee and mess with you by running backwards.  Maybe you should just stop it and restart it or buy a pusher prop.