I prefer remanning a bad engine to rebuilding. You really want to rebore and re'spec everything.
It is kinda an opinion. But if you are having serious engine knocking, then you are doing physical damage to pistons. Seals. Rings. The physical cylinder itself. You really want to get in there at a shop and get everything back, if possible, to factory quality. Knocking is the product of violent pre-detonation in your engine. That is a TON of explosive kenetic energy ripping into every engine component. If it really is knocking, and knocking seriously... I wouldn't trust a single component in that engine.
A rebuild kit usually ignores a lot of those issues. It may or may not have new pistons. Get what I am saying? I think your engine needs a complete breakdown and to go through a remanufactoring process. That is costly and you could as easily simply buy an already remaned 22r(e) from various companies. I like Jasper engines. They come with a nice warranty.
But.. again, they cost 1 to 2 grand and you have to do the install work yourself, or pay someone; which is another chunk of change.