Is your trailer level with tow vehicle ? It needs to be near level (on level ground) or u will have some of the problems u describe,.....

Trim it High and Let it Fly ! !

You're over thinking it. Just try Tracy Lee's advice and I bet you'll be happy with the results.

It's a 99 Dodge Dakota pickup truck and its pretty low (not like an F150 or Silverado). That might help too. I've been gunning it level versus trim up high lol.

I have a Tracker with a 9.9 and had the same problem when I got it. Since you have a bigger motor this will be easier for you.

What I do is get the fenders about a inch or two out of the water and then as you approach the trailer try to aim the point of your boat at the roller on the winch. When you feel the boat hit the bunk boards give it a little gas and it should run up to the winch.

Different ramp angles make having one set reference for the wheel wells kind of iffy but for most of them you can sight them in.
By the way there are some boats that just don't seem to want to load properly. I've seen it often that people have trouble getting all the way up the trailer at all times.

I used to have a boat that had to be just right or it would not load all the way. In that boat I would put it on the trailer and have my partner get off and winch it the last little bit while I gunned the motor. When I was by myself I would put it on the trailer and get it as far as I could. Then put it in gear and get off and hand winch it myself.

Sorry, mine is actually a 175txw but there is only 1' difference. If your trailer is level with your truck on level ground if you do exactly as I explained you should hit it every time.

I actually looked at your boat closely in your signature and see what your talking about. You have a new EZ loader tracker trailer with rolling guide bunks where as mine are stationary guide bunks. Don't worry so much about those being out of the water. If you hit the trailer straight (or even close to straight) their purpose is to center your boat as it comes out of the water. Think of it as a person standing on either side holding the boat as you come out of the water.

I had a similar problem, and it was significantly worst on ramps which are steeper than normal.
I experimented with different combinations, and finally discovered that by using a ball mount, for my hitch, which placed the ball exactly 2-1/2 inches lower than the original, resulted in a level of trailer to boat floatation that allowed proper contact in all points when loading the boat.
I suggest experimenting with different amounts of "ball drop" from the one you have.

You're going to encounter different challenges with loading that will be due to the angle of the ramp. With a very steep ramp you may need to load in two stages. First get you boat on the trailer and hook to the winch. Then you may need to pull the tow vehicle forward so the bow will be able to rise above the rubber V. It can be frustrating for all of us at times...you're not alone and it isn't easy at every ramp. Just chill and you will learn more and it will become easier.

forget about the rollers - just back the trailer in a little farther and use the bunk boards for your target - your boat will aline itself on the bunks and should drive right up to the winch.

This makes a lot of sense. Back it in too deep on purpose to wet the bunks. Pull it out to where you think it needs to be. Drive on staight on the bunks and it should line itself.

I didn't even know my trailer had a back roller for awhile. Back in a little further to wet the bunks the first couple times if you want. But after that, just use the bunks as your guide. I typically "power load", which means I drive the boat up and let it settle on the bunks and use the motor to get that last 6 inches to a foot to get the eye up to the bow roller. Some folks think that it can mess up your prop, but that's how my dad did it for many, many years, so he's already messed that prop up if that's true. Maybe I'd think about not doing it if I had a new boat? Anyway, that works easy for me.

Is it bad to winch the boat up 2 feet or so every outing? Or is there any side effects or long term issues with using the winch often?

I sometimes have the same problem. I have a 17 ft xpress wuth a 90. I never worry about it. I always leave the trailer a little shallow, idle up until the boards stop the boat, get it straight, and give it the gas. Sometimes it makes it up all the way, sometimes it don't. It only takes about 3 seconds to finish winching it up if it don't make it. It's not a big deal to me.

Back your trailer in until the water is just at the top of your forward bunk tops. So the forward bunks are just barely submerged. When you see where your fenders are then you will soon be able to put it there second nature. As others say...practice.