I have just recently done the same front R1 & rear R6 suspension conversion.
On the front, the R1 USD forks are about 40mm shorter than the originals (I have used 2000/01 5JJ version), so I suspect that your front end will naturally be lower now anyway.
If you have changed dog bones on the rear to make it same height as original, I would expect that you would need to lower the rear in order to come closer to the ‘even keel’ of the original setup. Dropping the forks through the yokes will only lower the front even more.
I can’t remember what the hole centre-to-centre distance is on the original Yamaha standard dogbones.
Does anyone out there have that ?
What is the hole c-c distance of the dogbones you currently have ?
Longer bar risers might be worth considering for a slightly more 'upright' ride ?