Motherboard is missing components

Hi
I have a 2009 Mac Pro that work until it was placed in storage for two months while I moved house. When setup at my new home it will power up everything such as fans and hard drives but it will not give of a chime, video or boot. To find the problem I began to follow the procedures laid out for these symptoms in the service manual, which is when I notice a few inconsistences between the manual and my motherboard. The service manual makes reference to certain diagnostic LEDS and reset buttons that my motherboard is missing. The solder points and labeling is on my board for these components but the actual items are missing. I have taken some pictures of my motherboard as well as images from the service manual so you can see what I mean.
It can be seen that the second image of my board is missing the 3.3V, 1.5V and 1.05V LEDs the manual shows.
In these two it can be seen that my board only has one button istead of five and is missing PGOOD RST, SYS RST, SMC RST and SYS PWR. Their are also various other points on the motherboard where parts seem to be missing. my question is if this is normal such as way in which Apple saves a bit of money as these parts are not crucial or if it is not normal and something i need to be getting in contact with apple about. i have made sure i have the correct service manual as well as looked for many hours for similar questions but found nothing so any help would be greatfully apprciated.

Can you give us a screen shot of the error message, and tell us exactly when it appears? What version of Acrobat, on what platform?

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