Moving the boat 6" can definitely have a noticeable impact on tongue weight and how the rig tows. For boat trailers (for some reason this is different than travel trailers), you're looking for 5% - 7%. Adjusting a trailer properly is not always just a function of moving the winch stand - sometimes you need to move the axles, as well.
I don't know where you are located, but the mention of a CAT scale above is a good one. Search around - you might be surprised that you have one (or more) in the area. Some large landscape companies use them, as well. Also metal scrapping places. I've never been charged more than about $15 and they never rush me out, either. I usually end up doing all kinds of weighing. Be sure to check the tongue weight at the COUPLER, not your tongue jack. You also need to check with the frame level. An easy way is to drop the front of the trailer onto the scale, with the tongue holding the frame slightly higher than level. Using a pre-cut a length of 4x4, drop the coupler onto the 4x, thereby putting the frame level.
You can do this with a bathroom scale, even if your scale doesn't go high enough. It's been a while since I did that (like 20+ years), but you basically use a couple blocks of wood that are the same height as the scale, set the blocks and the scale, say, 3' apart, then use a piece of wood to connect the two of them. Then drop the coupler onto a 4x4 like above. Depending on where in that 3' you put the 4x, the weight seen on the scale will "x" % less than the real amount. You then calculate the actual weight, based on how far the 4x is from the scale. Google it - I'm sure there is mention of this, along with the calculation. It's not hard, by any means, I just don't remember it well enough to say.
NOW, all that being said... if the rig currently tows well at highway speeds (including a little exaggerated lane-change maneuvers)... Just cut the bunks off. Easy peasy. Peel the carpet back, then your choice of a zip saw... circ saw... hand saw, etc. Easy.
EDIT: Oh, it's better to have extra tongue weight than not enough. Assuming the tow vehicle can handle it.