@Ceaser,
You can't expect a computer system such as this with all its socketed chips, daughterboards, etc. to NOT come loose in transit. Hell, A500's and A2000's have had to have their Agnus chips reseated after UPS hauled them away from Commodore back in the day!
The seller looks legit and the screen did have Workbench up. If you are going to own an Amiga system, you MUST NOT be afraid to remove and reseat chips and components. That's common sense 101 when dealing with vintage computers.
Using a very small flat blade screwdriver, you may carefully pry up one end of a chip (I.C.). When you feel the pins have moved up slightly, you may then press down on the chip to reseat it. That "fixes" most chip/socket problems. If not, the more aggressive thing to do is remove the chip completely (working your screwdriver from one end to the other carefully and slowly) and press it back in again. Assuming the legs/pins did not need to be cleaned. Look for oxidation on the pins and if necessary, light sand paper or better yet: a fibreglass brush may be used to clean them up.
The Busters people talk about require a PLCC chip removal tool (if it's not directly soldered to the board that is). Rat Shack sells them for $10 and are a necessity. NEVER try to remove one of those square chips with a regular screwdriver!!
Other scenario is that the capacitors on both the 040 card and audio sections could have been soldered in backwards. + <> - got reversed, causing the caps to blow up and leak their acidic spunk all over the board. VERY common when buying someone else's old Amiga 4000's.
One more thing: be sure to tighten the motherboard down with all the screws AFTER you've determined that the capacitors did not blow up. Good grounding is necessary for our Amiga's to behave properly. Removing the 040 board, observing that all those TINY pins are in alignment and reseating *IT* is also something you're going to have to do...
BTW: Great price you got there! Well, if you can get it to work that is ;-)