I just pried the seal out with a small, straight screwdriver, with the tip covered over by electric tape. Just take your time, and loose the screwgee ASAP so you don't scratch anything. I would use toyota seal if you didn't last time, and find something soft and flush to tap the seal in better. I didn't mess with the housing...just left it in place.
Plan on resurfacing the flywheel, and I'd put a new clutch, pressure plate and throwout bearing in, and maybe save the old one for an emergency spare (or toss it if it's close). It would be worth the extra hundy to not have to drop this tranny again for at least a couple more years.
I'm not sure what you'd do if the crank is scored...others will though.
1992 Toyota Pickup, 2WD, base, 22RE, 5-speed, 144,000 miles.