Not only am I new to this forum, but I am also new to working on old vehicles, let alone a Y-block. Some back story of my truck. Before my father passed a few years ago, he started the restoration of his '59 F-100 with a 292. He took the motor to a local engine shop and had them do a complete rebuild of the block and heads. From what I know, ha had them replace all the original internals with new of the same spec. The only thing I do know is that he had them put in a "mild" cam, but I don't have the specs on it right now. When he got the engibe back, he replaced the old 2 brl intake and carb for a stock "A" code 4 brl intake and a Holley 600 cfm (I know its bigger then needed but it's what dad bought) and installed a set of headers. The only thing that has been changed since this is I installed a Mummert aluminum intake and my brother switched it over to electronic ignition. We are trying to put the finishing touches on the truck and have ran into a fairly big issue in regards to the timing. We tried setting the initial timing using vacuum first but could only manage to get about 12 on the gauge at idle (@650 rpm). When we put the timing light on it to check where we were, it was about 42° advance. We know that this is way off, but are struggling to figure out why. We verrified TDC for #1 cylinder and checked the rotor position on the distributor and it was good, so we are pretty sure the distributor is in correctly. I know very little about distributors but the rotor seemed very loose. I am not sure how much rotational play there should be in the rotor. I also know that the cam timing is set on this engine using the 3 'oclock method with 12 pins between the marks. I think that if this was off, the engine would not run at all so I am pretty sure this was done correctly also. I don't know anything about switching to electronic ignition, but is there anything that could ave been done wrong? It appears that the original distributor body was used in the switch.

I assume I have a lot of missing info to figure out what is going on, but hoping there are some Y-Block gurus out there that can point me in the right direction. Any and all assistance is greatly appreciated.

You probably have a combination of problems.  It doesn't have 42 degrees of initial timing.  The engine simply would not turn over if it did.

Your method to set initial is not correct.  It is not vacuum that you use to set timing.  You set it with a timing light.  You also need to be sure that the vacuum advance is disconnected and the vacuum port plugged when setting timing.  If you do not, it will add timing to the engine, making it appear to have more than it actually has.

Another reason you might see higher than actual timing is that the damping mass has slipped.  That is the part with the timing marks on it.  If the damper is original or an old rebuild, then that is high on the list.