First, that link is to Edition 6 of the service guide from 2005. There is later versions, such as Edition 9 from 2014 which I am looking at.
Should be available on Keysight website and others - but I can provide if you would like it.
In both editions on page 106 "Power Supplies", it states:
The reset output of U553 will change to logic LO when the unregulated dc input to the regulator falls below 5.5 volts.
So, when you say:
The transformer does seems to be a bit low and is reading 4.6V but this seems close enough to 5V to not the cause of the problem.
Which "transformer" output are you referring to, and what exactly is measuring 4.6V?
There are two 5V rails in the power supplies schematic on page 9-15:
- the output of U751 called "+5V_0" earth referenced power supply - going to sheet 7 (page 9-14)
- the output of U553 mentioned above called "VCC" for the floating logic power supply going to the other sheets.
U553 also outputs XPONRST which resets the main mcu U500 and ASIC U501 on sheet 6 (page 9-13)