Help, new transmission now everything is bad

Hi, I need help. On monday I put my 99 pont. Grand prix gt, 112,000miles in the shop for tune up and mystery whinning noise. 1200$ later, I had rack and pin, new power steering pump, tune up, 3 tires, diagnostic -(all clear) and told tranny needed looked at. I want u to know my car was running fine. Just a lil bogged down, hence the tune up. Wednesday car in trans shop, got new tranny and car back fri. Now its all messed up. Motor is mising, trans is slipping, clicking noise coming somewhere between dash and steering column when I shift to park, not smooth shifting, and lights on dash not telling me what gear im in. Oh and now my engine light is on. And car idles and runs jerky. 3,000$ later car back in tranny shop, and telling me its my tune up? What is going on? If u have any idea please let me know thank you