Q&A

Yes, the truck did run afterwards, it ran rough but it did start. In the meantime I took the cover back off to make sure the chains are tight and in tact. Even if the timing was off wouldnt the truck still start? Maybe causing a backfire noise or something? when I Replaced the chains and guides, can that throw it out of timing?

You have to follow procedure to set the timing and put the chains in the right positions for the cam phasers to operate properly. You could have it 180 degrees in the wrong direction on one bank, compared to the other. I know highly skilled Ford technicians that have been working on engines for 20 years that consider it difficult to replace chains on a DOHC 5.4L engine. I'm only saying that unless you have replaced many before and are an expert at it, and have the special service tools to do the job, and the shop manual to follow to the letter, you are risking issues. No offense directly to you as I don't know what your skill level or experience is, by any means. You certainly completed a major undertaking by replacing the guides and chains on this engine.

It is definitely possible to cause a no-start by being out of time. Unless you diagnose it with the proper diagnostic equipment, you may never know for sure.