Unless you're going absolutely nuts with power don't completely throw the NV3500 out the window. It's usually much cheaper to obtain, takes cheaper oil, shifts faster, and is much lighter than the NV4500. If you get the 93-up version, they're not bad transmissions. They just start to fail with severe heavy-duty use or with tons of power running through it. Just think about what you will actually do with the truck before deciding.
For a 1995 truck, you'll need to get a 92-95 version of the NV4500. The 96-up version uses an internal slave setup, and the master cylinder mounting is incompatible with the firewall of the 1995 and it's kind of troublesome to find a solution. They also changed the transmission to bellhousing bolt pattern after 1995 so you can't just get a 96-up trans and put an earlier bellhousing on it. FWIW, you'll find it extremely difficult to get a 1995 version. It has closer ratio gearing than the earlier ones, gets the updated shift tower, but still retains the external slave bellhousing, and it is 1 year only and sought after.
For driveshafts, try your best to find a transmission that has a slip yoke output. You'll probably need a different driveshaft regardless but it's much easier than trying to make a 2-piece driveshaft work with a fixed yoke trans, especially on a short truck. You'll need a new transmission mount but the crossmember should be the same.
As far as electronics, the engine controls are different for manual vs automatic transmissions in 1995. While this doesn't make the swap impossible, there may be a few things out of sync with how the engine runs with the stock computer. If you switch things up, it's one less thing to worry about though.