It sounds a bit like you've begun the job by starting in the middle!
As you already know, it is possible to remove the lowers after unscrewing the large Allen screw in the bottom of the fork lower. Here's the fly in the ointment: You need to access the top of the damper rod and secure it with a socket and a 14-in extension to properly reinstall the assembly. To do this, you will need to remove the upper caps and the spring-wire circlip that retains the spring assembly.
By loosening the triple clamp pinch bolts, the upper stanchions can be withdrawn. If stubbornly stuck, a wooden wedge may be carefully tapped into the pinch bolt openings to relieve clamping pressure. Carefully!
Further work may be done with the stanchions held in a large vice and padded with wooden blocks. Watch for the damper rods and springs as they fall free from the stanchion.
The fully assembled fork legs may be refitted up through the triple clamps.
Did you purchase new felts for the rubber cups?
Good luck. Any more questions, just sing out.
Monte