Hello, and welcome back to the world of Amigas. I'd say you never fully left because you kept your 1000. I had my Amiga stuff in storage a few years, too, until nostalgia got the best of me. Now I have a room full of 'em.
I have had a Microbotics 68030 @50mhz accelerator in my 1200 since those things were new, and it also gets a little toasty. Because of this, I leave the trapdoor cover off and and a small fan rigged to blow across the opening. It's hidden underneath the little monitor stand I have, and I've raised the 1200 a little with some rubber stick-on feet to allow better airflow.
Before doing all this my 1200 would lock up when left running for a long time in all but a cold room. But I've been doing it this way forever and it never locks up anymore, so thermal problem solved.
I'm running with Kickstart 3.1 chips and OS3.9. One bit of weirdness I noticed with the Indivision flicker fixer in my 1200 is that I will get artifacts in the screen when running large fields (like Web browser background) in pure white. If I tone it down to a light gray, the artifacts go away. I sometimes still see them in my white menus, however. May have to adjust my palette some more.
One day I'm going to try the CF card replacement for the hard drive, but for now I'm using a 2.5-inch IDE drive swiped from a broken iBook. The capacity is huge by classic Amiga standards, but the CF route appeals to me since I'm now running two other classics Amigas on USB memory sticks.
Have fun, and good luck getting your 1000's floppy problem solved. The only spare parts 1000 I have in the closet has no floppy whatsoever, so I can't help there.
