No, I don't think you have made your bike unsafe, though the handling has changed. There are a lot of discussions about stem length and a lot of responses have been that for most of us casual riders, you will get used to the changes pretty quickly. I have never, on either of my bikes, no matter how they have been configured, felt stable on the hoods, only stretched on the drops.

Having similar difficulties with saddle fit, and reach, here's what I have done:

*Swapped a lot of saddles and change riding posture
Change my posture because I have more of a swayback. Tightening my stomach, rolling my hips backward just a hair, made the whole seat fit-thing much less problematic. I know, rolling hips backwards is opposite what most people need to do. So are you slightly swaybacked in the drops, very straight, or slightly rounded?

*Moved seat way forward to put me in a comfortable position of the pedals. Should put on a zero-setback post and center the seat on the rails again. Weird, but turns out the cranks are 10mm longer than my Sekine.

*Shortened and flipped the stem from 100 to 80. Same 7 deg angle by chance. Now I have a shorter reach, a little more room for height adjustment w/o screwing up reach too badly. The whole bike feels so much more comfortable and stable because of weight distribution and posture.

Maybe a perfectly fit bike frame would have alleviated some of the problems, but not my swayback.