I'm thinking of getting a do it jig mold and I am already of thinking of ways I'd like to modify it. 

 

My question is while modifying the mold with a dremel if I was to take off to much material and the lead is now able to seep into the modified area is it ruined or can it be repaired with something like the jb weld epoxy putty?

 

Also one of the modifications I was pondering was modifying the mold to accept both horizontal and vertical eye hooks.... has anyone done this? Can it be done?

Yes yes and yes....generally speaking most modifies I've seen done with a dremel use red rvt gasket stuff from AutoZone 

Here is a poison tail mold modified for flat eye hooks and a shaft to make spinnerbaits/chatterbaits/etc. Don't be afraid to mod the mold- you can correct it if needed as dsqui has indicated.

 

One way a journeyman mold maker would repair it is with an insert. Drill a hole in the area of error and insert an aluminum rod same size or a bit smaller. i.e. drill a 15/64 hole and use a 1/4 aluminum rod. Heat the mold a bit and freeze the rod. It will slide in due to expansion / contraction. Peen the insert and it will stay in there no problem. 

 

The best fix would of course be to have it tig welded. 

That red RTV silicone can be found in a lot of my molds as well as JB Weld.  They both work depending on the circumstance.