Now is time to do it right. seems you bought someones project gone wrong, or the best he could do.
the correct way, get a welder or a friend with a welder, and get the correct panels if replacing or get to removing the old and rewelding correctly. remember body welding is a trick of it's own and not fast, you can warp the panels with to much heat.
A bit of advice
Owning a pristene CJ is not easy, nor cheap. You can do it correct, or do it like the PO and off it on someone. A pristine CJ is a thing to be fiercely proud of. You now need to make a decision, correct or hacked. It is up to you, correct means paying someone or doing long hours on and under that rig getting things correct. I sub out axle work and do all else myself. When I pill up with one of my Old paint and primer jeeps, you look at it like it is a pile, but soon you see the body is 100% and the mechanics are 100%. I love wheeling those show TJs and JKs into the dirt. I cannot stress how important doing it correct the first time is, Most of the rebuilt CJs I see have temp patches in their body, or need a new this or that and have a great paint job. They break down on trail a lot, then there are the guys with everything correct that do trails all the way, I am the guy who just does not care to paint his rig as I get an obscene pleasure out of driving what looks like a bomb, that can pass you ontrail. My 67 has rebuilt axles front and rear, just rebuilt the tranny, about to do the tcase, body is sound but needs a new hood, I am making custom bumpers for, have replaced the obsolescent clutch system. am slowly redoing the interior and work on the thing most weekends so that this spring when I bring it out, I will be feircely proud of the beast.
Make your decision on how much you want to be proud of that rig. Thar body work is just one of 100 projects you will find over the next few years and it will never end, but you will have a reflection of yourself i it.