Do you think that it would be easier to get the color that I want with an acid dye and varathane's crystal clear water-based urethane? Then there wouldn't be any influence on the color by the urethane.

I think the influence of the natural varnish color on the outcome is prolly negligible ... I certainly haven't noticed it on my boat.

I've never tried acid dye but lots of builders use it with Cory's Goop. Personally I think it sometimes looks a little uneven but I wouldn't say it looks bad.

Lots of builders report problems with water based varnishes on nylon but I recall some folk had no problems with it. If that's your plan I'd research it out first on the Qajak USA forum.

Ken Blanton