2004 Ford F-150 Catalytic convertor Question

I just bought a 2004 F-150 Lariat 4x4 supercab 5.4L Triton with 140, 000 miles that needed a new engine had one put in for $ 7000 has the 3year 100, 000 Ford warranty brand new from ford not a rebuild, anyway got it back noticed a clattering nosie when I accelerate had it checked cause also the check engine light came on, so the place that put the engine in STI in Brooklyn park mn said I had a bad catalytic converter right side and I maybe had a few months before it had to be replaced cost $1800 for new OEM Catalytic converter and $160 labor, so that explained the noise the check engine light was on he said cause I had a O2 senser out, I had the O2 senser replaced $120 later took the truck home drive it for 300 miles now I noticed the check engine light is on again its sunday today so they are closed cant take it in till tomorrow. Hoping its not another O2 senser. So what im wondering is what can I do about the bad Catalytic converter the guy at the shop said I had to go with a OEM Cat cause something about any after market ones wouldnt work right and it could damage my new engine and maybe void my warranty. He also said I could get a used oem from a placed that legally dino blasts catalytic converters and tests them in St cloud mn cost $900 and $160 labor. Ive done a little research and I hear alot of people say to go to a muffler shop have them put on dual exhaust and one mega flow Catalytic converter and get rid of the two cats anyone have a opinion plesae let me know what I can do and will I keep blow O2 sensers if I dont get it replaced, is there something my mechanic could of done to my truck when he replaced the engine to either ruin my cat on accident or my O2 senser?