dl_racing427

Those 5.9's are common as dirt.
Find a shop that specializes in diesel pickups, and that has a good reputation among local Dodge groups.
It's not that complicated to ream and install valve guides, as well as a standard valve job.
Aftermarket should have you covered as far as valves, springs, retainers and keepers.

Good luck.

That looks to be a very common series of Molex connector.  I've disassembled those many times.
A thin pick can be used to depress the tab and remove the pins.  Molex also makes a special tool for this.
Search Youtube for instructional videos, I'm sure you'll find something explaining the connector type.
Once you positively ID the series, pins are available at most electronics supply houses.  Try Digi-Key online.

Another option is to cut out the entire opening, fabricate a sheet of stainless perforated metal and rivet it over the opening.
Just be sure there's enough open area to let the engine breathe.

The front seal leak on the engine is the easier to fix, though if it's only a drip or two when parked, I don't know as I'd worry about it.

It sounds like your tranny leak is worse.  That one would require pulling the tranny to fix, which you may want to leave to a shop.
I don't know what the Allison tranny weighs, but I'm sure it's significant.  Without the proper equipment to handle it, it could be a somewhat dangerous job.

You may want to wait until you drive it a couple more times to see if it improves, but I agree, if fluid is being sprayed on the undercarriage, it's big enough to be a concern.  Definitely keep an eye on the fluid levels.

I was going to suggest that, but the Gary's beat me to it. LOL

Drill an 1/8" hole to mitigate the stress riser, and fill it with a dab of RTV.