the shift housing has the rubber gasket under it. but the metal spacers that should be placed in the oversized holes of the gasket over the bolt holes are missing. that is why the cover is loose. maybe they are on the bolts like washers?
as for the rear brakes, when you pulled off the left drum, if it came off easy its because the shoes were not adjusted correctly. they should ride pretty close to the drum. there is a wheel on an adjustment thinggy toward the upper inside part of the shoes. you have to turn it from a little window on the inside part of the cover. its not easy to adjust. but when the shoes dont make contact with the drum, little or no fluid will come out when you bleed the brakes. you must have adjusted that to make it work, or you put it back together wrong?
the starting problem could be the wire that runs from the igniter/coil to the magnetic pickup in the distributor. engine heat can make it brittle, it can crack or break. it can still work, just not very well. if you wiggle that wire and it either starts right up or wont start at all, try cutting it and splicing in new wires the same length. you done good so far, you have sweat equity, and you learned a lot. these are all typical toyota down the road problems. keep after it. its like the last turn in the quarter mile foot race. be proud of all you have done so far, this is a great truck and you have almost got there.
water pump, starter, timing chain, alternator, coolant hoses, ujoints, air cleaner, and a few other small jobs over the next few years.
put some wd40 or 3in1 oil on the tailgate latches. there is a panel on the top inside surface of the tailgate that comes off. check in there. check to see if the strike plates for the latches line up with the latch pins.