Do they affect the numbers on a dyno. I was told that gears alone will show a lower hp and tq and I was also told that a high stall will affect the numbers.

Yes gears can show lower HP on the dyno and some aftermarket converters can do the same thing but by locking them up in the top of 3rd on the dyno it should take the converter out of the measurement.

So when you look at someones dyno you have to take A LOT into consideration. gears, rear end (10bolt-12bolt-9"), converter (locked or unlocked), etc.

Anything that takes you further away from 1 to 1 with your engine will show you less hp.