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I am attempting to refinish a guitar I built when I was 14 pic 1. I have a small issue that I do not want to become a huge issue.

The output jack is in the front of the guitar, next to the knobs. At some point someone tried to use it without a 90 deg patch cord, and stressed the wood. There are a few small cracks. Pic 1.

The second pic is one that was left unfinished years ago, and split pretty bad. I do not want this to happen to the guitar in pic 1.

I think the split in pic 2 was caused by the finish being removed from the front of the guitar, but it was still on the inside of the cavity. Causing uneven expansion/contraction.

I plan to strip the lacquer off of the guitar, dye, and fill with z-poxy. Then re-coat with lacquer. If I get the finish off inside the cavity, will I be safe enough, or is there a way I can get some sort of glue, or sealant in the cracks. I'm looking to prevent a split, while not having anything on the surface that will effect the dye.

I will be dyeing with black, then sanding back, and using a red/yellow mix. I'm afraid of it splitting while the dye is drying. Water based aniline from Lee Valley.

Your cracks are not caused by the finish (or lack of), in my opinion.
Suggest you wick thin super glue into the cracks, or simply veneer the top - which will add strength.
What kind of woods are you using on these 2 guitars?

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"Act your age, not your shoe size" - Prince

The one I am working on is Australian lace wood. The cracks in it are caused by the jack being twisted and pulled on.

The other one with the wide crack was a maple veneer, which split a day after taking the finish off the top. It has cupped out as well, which is why I believe it was caused by moisture due to one side being sealed and the other open. It was just left in the wood shop at school. It's the lace wood guitar I'm worried about. I think its a little thicker than the maple veneer on the 2nd. So it should be ok.

I will try wicking some glue into the cracks and see if it holds. If it does split I will just throw in a plate for the output jack similar to a strat. That should cover it.

whoooo, not superglue.
This looks like it needs strength and a slow cure epoxy glue will work better if a minimal amount is used, otherwise it will run through to inside. Use a small microwavable dish, heat for a short time just the dish. then using gloves take the dish to the workshop where your guitar is waiting prepared, test the dish for heat with hand , if its too hot to touch wait to cool a bit. - add the epoxy to the 'hot' dish and see it melt to a thin glue, add hardner and mix, squeeze down small amount into cracks and damaged surface with a small tool- plastic , remove excess glue as this will go very hard when cured.
leave for 2 days before rebuild

i've used araldite slow cure general epoxy with good results. Normally workable for 2 hours...
but with the heat its more like 20-30 min

Other solutions can be found on youTube, some are terrible. Luthiers have good info (here).