"I" would endeavor to at least find, if not correct, any running problems BEFORE you rip the engine out of the vehicle for extensive service.
Otherwise, you'll get the "new, rebuilt" engine re-installed, it still may not run right because of some as-yet-undiscovered root problem, and you risk screwing up the rebuilt engine due to a faulty ignition system, faulty fuel system, faulty exhaust system, failed ECM, corroded wiring connectors, or whatever the problem(s) turn out to be.
OTOH, if you can say with certainty that the two misfiring cylinders also have poor valve seal, or oil-fouled plugs, or whatever, you stand a chance at correcting the problem during the overlhaul.
Keep looking!
Otherwise, you'll get the "new, rebuilt" engine re-installed, it still may not run right because of some as-yet-undiscovered root problem, and you risk screwing up the rebuilt engine due to a faulty ignition system, faulty fuel system, faulty exhaust system, failed ECM, corroded wiring connectors, or whatever the problem(s) turn out to be.
OTOH, if you can say with certainty that the two misfiring cylinders also have poor valve seal, or oil-fouled plugs, or whatever, you stand a chance at correcting the problem during the overlhaul.
Keep looking!