Entering the service menu, choose Alignment.

the radio will show PROGRAM mode.

Proceed in order, set the Squelch level.

Computer shows this...

Radio shows what frequency to set your scope to.  (this case 350.125)

I am generating 1KHz of tone, at 1KHz deviation on 350.125MHz with the power at .30uv.

Align the deviation.

Align the oscillator.  Note this is before I refurbished the radio.. it's at 71..

The scope shows a freq error of 784Hz, not bad, not great, still out of alignment!

Dropping the frequency warp down to 68, results in..

A frequency error within spec of only -87Hz!

Align the high power to a watt or two UNDER the rated power level.

Align the low power to whatever you require...

Low Power Alignment, at 900MHz we opted for 10w

10 watts at 901.9875MHz. 

Alignment of your radio is critical to it's proper operation.  Much of these settings are in direct relation to
current draw through the capacitors you changed during the refurbishing process.

You wouldn't put a brand new set of 22" low profile tires on your car, without having them balanced and aligned! 
Don't re-cap your radio with aligning it, or having it aligned!