I prefer everything about the 94 except for the fact that its a PITA to load compared to the 336. Is there an way a 94 can be modified to where the entire round can be pushed past the gate and topped off like the Marlin?

I think you're doing it wrong. I have a 94 in 357, and at first I thought I couldn't top it off. At least with mine, it can. Instead of pushing the round at the front edge of the loading gate, try pushing the round against the back end of the gate, pressing down as you slide it forward toward the gate opening. This works for me perfectly.

But if that doesn't work, go over to homesteadparts.com and buy a new loading gate. When you get it, look at the back and you will see a rib along the back of the gate. It has a sharp edge that catches on the back of the round. You will have to polish that  a bit so it can push past the last round in the magazine.

Here is a link to a discussion with a picture of the finished product.

the only winchesters I have had that would not top up had worn loading gates. they are easy to replace

I bought this one pre-owned but unfired so wear is definitely not the issue. I can top it off but it's a two handed affair of pressing the loading gate down with one thumb and cramming the round in with the other. It's caused by the way the rim of the last loaded round slips back behind the front edge of the loading gate.

After loading and cycling the Winchester about 500 times today I've come to the conclusion that it just needed to be broken in. It was still tight since it was basically a new gun but it's much easier to load now.

When loading the mag tube push the cartridge about 90% of the way into the port with your fingers, then use the next cartridge you are going to load to push that round the rest of the way in (and start that next round in 90% of the way and and repeat).

Try it, you'll see/feel why that method is a little easier than letting the gate snap shut on every round.

This. Plus I use my left hand to cradle the rifle and my lower fingers to secure the rounds in the loading gate while I grab a new round

I use this on my 92 as well. Sometimes the tension of the mag spring will pop the round out of the loading port.
Also I have fat fingers and use my pinkie to set the final round. It's the only finger that will fit in the Port

Try smoothing up the edges on the parts and port.   You can probably shorten up the magspring a bit.   Look for some 1894 tuning tips on the web.

I have this same problem.