Unfortunately it's nowhere near as easy to just change the floor panels as in, say, a CJ, due to the unibody construction of the XJ. Your best bet is to find a really good bodywork guy to do the welding. Remember, the floor is a structural piece, so only attempt it yourself if you're sure of your welding skills. It's one of those jobs that's best done right first time, so take your time to get recommendations and see the work of different welders.
It will cost more than patching it with glass fibre or doing the welding yourself, so if you want to save money, it's easy enough to remove the carpet, console & seats beforehand, so he can just get stuck in. I know this contradicts quite a lot of what people do to their rigs, but IMHO you're better off doing a proper job than a bodge.