It sounds like you haven't disconnected the shift linkage. Go ahead and put a couple of bolts back in the lower unit and tighten them back up. Next look at the diagram I have below. #30 is the intake screen for the water pump & must be removed from each side of the gearcase. Inside this cavity you will see the shift linkage held together by what looks like two nuts (#s 49 & 66). Using two wrenches unscrew both nuts from each other.
Next push the top nut up the shift shaft until you can see the little plastic ring wrapped around the bottom of the upper shift shaft (#73). You will have to move the shifter to push the shift rod down as far as it will go, i believe this is forward gear but it may be reverse. This plastic piece is what holds the upper nut on the shift shaft. Remove it from the shift shaft and put it somewhere it won't get lost. Now move the shifter so the two shift shaft separate enough that you can get the upper nut off the shift shaft. At this point you may have to unbolt the lower unit again to get the shift shafts far enough apart. Once the nut is off the shift shaft you can remove the lower unit from the engine. Let me know if you need any other assistance.
Marine Mechanic
11 years experience working on outboards, inboards, sterndrives & pwcs