Strange issue...Shift shaft stuck in upper unit and came out of lower unit, need help!

Hello, I have a strange issue and I have searched online and through forums for help and haven't found anything related to my issue and I'm hoping someone might have some advice.
So for starters, I have an old 1969 Mercury Thunderbolt 650 that I bought from an old man who had owned it since purchased, but he said it had been sitting unused in his barn for about the last 25 years or so. t looked to be in good shape from outward appearance and I couldn't pass it up for only $100. Well when I got it home, I found out firsthand what happens when a motor sits that long, because all of the grease everywhere has turned hardened and was rock solid almost, and the gear oil in lower unit was a gunked up mess. I sat out to do normal maintenance on it by removing all of the caked up hardened grease everywhere and adding new grease to the motor up and down. I drained the gunk from LU and dropped it to replace water pump and impeller, only problem was it was stuck, as in lower unit would not pull away from upper. Finally after a few days of adding penetrating oil and working at I got the LU off, but I had a new issue now, because the shift shaft is stuck in the upper unit and when I pulled off the LU the shift shaft pulled away from it and came out.
So now I'm stuck with the shift shaft caught in the upper and the LU being stuck in forward and I can't get the shift shaft unstuck.
I know already the headache I'm gonna have getting it seated right back into the LU, but have to get it out of the upper unit first and I'm at a loss. It's like it rusted into the upper or something.

Any help or advice from anyone, I'd really appreciate it.

You have disconnected the shift shaft upper and lower halves ?

Yes, I have the upper still mounted on boat with lower removed.

It sounds to me that you have to separate the middle section from the engine and give it a complete cleaning job. Soaking the engine bottom in kerosene will loosen up the gunk and when you have it cleaned up , a good amount of penetrating oil where the drive shaft goes into the block may help as well.
If you get lucky you can clamp a slide hammer onto the drive shaft so that the sliding end with the weight below the shaft and ram the weight down a number of times. it may loosen the drive shaft enough to come out.
but you will still have to take things apart to clean them up.

Okay, I will give that a try. I've already tried clamping a handheld vice to the middle of shift shaft and tapping it with a hammer, but was afraid of bending it if I hit it to hard. Your way with a weight seems like a better idea since it would even the force all the way around.
Am I right in assuming that the shift shaft also has splines that fit into the shift linkage in the upper the same as it has on the bottom?