From your comments about flashing buttons I assume you are using Mach 3 as the controlling software and that you have set up all the pins and ports as per your documentation. If your machine came from UK, www.syil.co.uk has both useful videos and sample profile files to assist with doing all of that.
The messages you have are two separate ones.
When you turn on machine the x, y and z axes will not have been "referenced" to their "zero" position. If you move all axes to an approximately mid position then click the "Ref all home" button the machine should move the table and Z axis to the home position and, depending on the settings you have made in the Config/Homing Limits Screen, should set the machine coordinates to 0.0000. (www.syilamerica.com has a useful short video to show how to set up and use the homing limits).
Incidentally if for some reason you don't want to reference - by clicking Operator/Set Nomal Condition you let Mach3 know that whatever current condition the system is in is the "Normal" one and it will only flash at you when something significant in the current setup is changed.
For the spindle:
In the Config menu, select ports and pins, spindle setup and make sure that under Motor Control "use spindle motor output" is checked. Your machine probably requires the "Step/Dir Motor" option. If using "Step/Dir" you don't need to activate the spindle relay options under relay control but you do if you use PWM control.
Having said all that your spindle problem may be more serious. In my part of the world (New Zealand) we now have a number of machines having troubles with spindle control at least some of which may be due to changes made to the machines to make them run on 230v. We are having great difficulty getting understanding or action from the manufacturer.
Upgraded spindle is not running at 3600rpm - runs at max speed of non-upgraded spindle ie 1800rpm
Speed can be controlled from front panel but not by any Gcode either from Mach3 MDI or in Gcode "program".
M3 M4 M5 commands work only intermittenty and sometimes with the opposite to intended result (eg M3 starts spindle CCW).
There is a lot of beeping and spindle may simply stop when under MDI Gcode control.
Our machine numbers are small but I would be interested to know if you too are experiencing these problems.
On the last issue you mention, the four diodes, I am not sure which ones you are referring to but again sounds like a power issue. In addition to the power supply there may also be an issue with the relay on the main spindle controller board. In a couple of instances here the original one (a 110v unit coupled with a resistor to pretend to be a 230v one) has died and needed to be replaced with a 230v one but before dying has worked intermittently. You may hear a buzzing sound at the back of the machine as the relay tries hard to make a connection when you switch it on and off.