Would installing a nosecone affect roughwater handling and stability?

Should not make any difference in most cases

What boat???? The lil Baja???? If so, you won't gain a thing.

Be careful, nose cones tend to add stern lift. If your hull does not like it, it will slow you down. Too much stern lift plants the bow and no amount of trim can correct this.

Wont gain it on the Baja? Are you sure?

The whole Nose cone situation confuses me

Yes, I'm sure, and like BadDog said, they can add sternlift. Thats why I took mine off.

You don't need a nosecone unless you are going at least 70mph and really more like 80mph. Also, they have to be put on PERFECT.

GRIFF can you give me details I put an Imco 2" short lower on my boat with the casted in nose cone and I'll almost swear the MF er is working against me

A nose cone lets water flow around the drive a little easier. It flows around easier and then does not "push" the drive down as much.

I took mine off because I just could not get the bow to lift no matter how much trim was applied. Basically, the drive didn't have enough bite in the water and when I trimmed up all I got was more rooster tail and rpms, and it didn't reduce the wetted surface of the boat. Taking off the nosecone helped slightly, but not enough. This year, I lowered the drive an inch and what a difference in the amount of lift.

Here's a pic of NOW after the changes. Before them I was running with 5 feet more boat in the water.

No, I actually just switched all my lower internals and had them put in a new DWP case. WOT Speed didn't change at all when the switch was made, so I doubt I would see much, if anything switching back.
Also, I have a single in my Pantera. The center of gravity is pretty far forward especially with a full load of fuel. I was 3" below the bottom and now I'm at 4" below. I even had the prop labbed and reworked fro more bow lift and reduced stern lift prior to dropping the drive an inch. Everything helped a little, but just not enough to get enough bow lift.