Sure have.
This is the same set up that is on my 1982 Merc 7.5, and I ran into the same problem after changing the impeller because stupid turned the shift shaft while it was apart. Here is how it was resolved after fiddling with it for way longer than I want to remember.
Speaking from an instance of installing the lower unit to the mid section and needing to align the shift shaft to the splined coupler. It sounds like this is your situation.
First off, it is much easier to fit the shaft to the proper shift range when the motor is upside down (same deal with my 9.8 shown below). Rest it on the top cowl, upside-down, with a blanket between the top of the cowl and the floor. I use a workmate table to clamp the mid section while it is sitting upside down to keep it from falling over.
Prior to turning upside down, remove the lower unit and shift the shift lever to the forward detent. After turning the mid and top sections upside-down on the floor, look though the mid section with a penlight and note the spline alignment of the most forward spline (like a clock hand position on the face of a clock).
With a channel lock plier, and a towel to protect the shaft, turn the shift shaft (on the lower unit) all the way to get forward gear (on the smooth part of the shaft, not the splined). Next adjust the shift shaft on the lower unit as little as possible to clock the most forward spline of the lower unit shaft to match the midsection coupler (for position after installation).
Lower the lower unit into the mid section carefully and verify shaft to coupler insertion with a light (also drive shaft and water tube). Lightly shimmy the lower unit with some slight left-right rotation until the shaft seats, and jostle the shift lever at the same time if necessary.
This procedure should result in all gear ranges again. It did for me.
