OP, can you chamber a x54mm round in a x39mm gun? No. Therefore, as has been stated, you need a different die set for each cartridge.
As to pulling the bullets, absolutely. But only do it if you are going to use it for hunting. Don't bother if you are only going to plink with it. I have been doing this for years and can squeeze excellent results out of a "non-precision" rifle. Most of the reasons they are "non-precision" are due to maintenance issues. Cleaning rods being dragged on the muzzle for years deform the mouth and cause inaccuracies. Easy fixes actually if you want to do it. I have taken two 4" SKSs andturned them into hunting rifles that shoot 2" or under by cleaning up the muzzle and standardizing my milsurp charges. With a 150gn bullet in the case, those SKSs are 200yd deer rifles. And most deer are taken at ranges far less than that.
On the same note, my 91/30 (again cleaning up the muzzle) will send doctored 180gn bullets worked up in a mil surp case into just over a 1" group using the original powder. This is easily a 300yd deer rifle and a 200yd moose getter.
OP, that one other thing mentioned earlier? Get a reloading manual and read it, twice. It will show you the difference between the cartridge sizes, it will tell you why you can't use one die, it will give you lots of info you need to do this.
One thing of great importance - PATIENCE - I just started out a young man in Rloading. NOT a patient man! Everything needed to be FASTER! Anyway, about a week after I had set him up with all of the gear he needed to reload military 7.62x51mm cases, a mutual buddy, another experienced reloader, drops in to see how he is doing, and finds the guy seating primers WITH A HAMMER instead of the Lee Ram-Prime I had given him, because that took too long. So, my buddy takes a primer, puts it on the floor and hits it with the hammer to show him how dangerous that was. Then he goes back and looks at the cases already primed and most are cocked off and none are seated to the right depth.
No more advice will be given to this young man until he smartens up. He even shoved a bullet into a case neck off centre and crushed the neck so that it won't chamber. He probably will not reload long. He was quite upset that it took 2 hours to completely process and reload 50 military brass complete.
He decided to reload because someone gave him 800 spent mil cases. He doesn't even have a rifle yet.