i'm running an 03 LM7 in my 1990 regular cab short bed, with a 4/6 drop. I'm using the stock 5.3 exhaust manifolds, Oil Pan, and all stock 5.3 belt driven accessories, EXCEPT the AC. I also used the Holley R12 ac bracket, to retain my old AC system. i havent had any clearance issues yet, and i live in south florida. the roads down here are awful. manholes sticking 4" up out of the pavement, potholes, bridge abutments, etc. never scraped anything. would probably be different if it was bagged. I also used the Transdapt LS swap motor mount adapters with the 1" setback. I probably could have gotten away with using the regular motor mount adapters, since i ended up drilling holes in the frame for the crossmember bolts, just about 1" behind the original holes. i used my original cross member, and driveshaft that came in my truck. But I'm using a 4L65E, and it mounts the same as my old 700R4. not sure how your manual tranny will work.