If the slave cylinder (not TOB) has fluid in it, the transmittion will not slide all the way in. You will need to use bolts to very carefully pull the transmission in. You will not be able to turn the bolts by hand after they start. There should be very little resistance when turning the bolts with a wrench. Fluid will run out of the slave as it is compressed. Do not try to depress the clutch and actuate the slave without the transmission being fully seated or you will damage the slave.
I think you just explained my issue when I did my clutch and for some dumb reason while laying on my back under the car I never thought to disconnect the clutch line at the master cylinder.... duh! So about 1 month ago I installed an ACT Twin Disc (which is super nice by the way, write up still to come) and I could not figure out why I couldn't get it to slide in that last 1/2" or so... actually I could get it to within an 1/8" of the engine block and it'd push back off. Since I could get it to go per se, I knew I didn't have miss-aligment so proceeded with the most sketchy thing ever... I pulled the two untis together with the bolts! I was super careful and went about a half turn to 1 turn max per bolt working my way around the bellhousing of my MT-82, I probably touched each bolt 30 times to do my best to spread the load and not pull the threads or break the block. Sweating bullets is an understatement. It's together and has been running flawlessly for over a month. If ever there is a "next time" I'll get a transmission input shaft and use it as an aligment tool, the plastic aligment tools are ... plastic.