I am pretty sure both of those are easy fixes take the door panel off and see whats broke or detached. Have you driven it yet. when they are both stock I think the auto is pretty close to the manual as far as performance.

Since I have 35's the manual tranny would let me keep it higher rpm's but with the stock tires the auto runs fine.

94 Rodeo 3+3 lift Red)
95.5 Rodeo 1" Body lift Dana 44' front & rear 4.88 gears 35"s 176,000 miles Optima Yellow top InexAir Co2
front winch bumper custom rear bumper, Hella 500's
2004 Silverado duramax