Click on the link, and it will show an exploded view of your water pump.
Official Case IH Online Parts Store and Case IH Catalog for Parts Search and Parts Look Up. Case IH Parts for Case IH Tractors, Case IH Combines, Case IH Tractors, Case IH Manuals, Case IH Parts
Sounds like the packing is leaking. It is behind, what you describe as the big brass bolt. That is the packing gland nut. You might try snugging it a bit if there are some threads showing. If that doesn't do the trick, a new packing is about 12 bucks. Manual says it's best to remove the pump to replace the packing. Pump mounting gasket is under 8 bucks, unless you can tap out a new one out of gasket material.
I'm still thinking you way overfilled the transmission. There is a check plug on the left side, in the area of the clutch pedal. Should be just below the level of the PTO shaft. Back up to post #39, and you will see where I posted a lube chart for the M. Click on it, and it will enlarge. Save it to a file, then you can print it off, maybe a couple of them, and put with your manual for quick reference when changing fluids.
I'm a little confused about the oil leaking out the front of the axle, and possibly getting on the clutch. I'm thinking you mean out the front of the transmission. That would require a seal that goes behind the clutch shaft coupler. It's been a while since I've had my M, and never had to replace that seal, os not sure if you can get the coupler out, without dropping the hyd. pump, which is a job in itself...
Most definitely check the oil level in the transmission, before doing all of that work. I think it may solve a lot of your problems...