Hey mchollan
I'm going to be a little more blunt...if the rear wheel (or especially the front) hits the fender under ANY conditions, then you have a serious problem!! The bike was designed with 4.9" of rear wheel travel. This likely left an inch or less space between the tire and fender at full compression. By lowering the bike 3", you have only 3" or so of travel before the tire contacts the fender...not good, and in my opinion, you should NOT leave the bike in this condition.
You have a couple of choices.
1. If you MUST leave the ride height where it is, then you must reduce the travel of the rear suspension. You can take the spring off the stock shock, and add additional rubber bumpers, likely an inch or so, so decrease the stroke of the shock. Then install a stiffer spring, and crank the rebound adjuster all the way up to full. This will leave you with a bike that has only 3" or so of rear wheel travel, which is not ideal...the idea is that the stroke of the shock must be reduced to prevent the tire from contacting the fender. This can be verified without the spring on the shock.
2. 2nd option is to raise the rear again, with different dog bones, and look at modifying the seat to gain some of the lowering you want. You can likely only drop the rear and inch or maybe 1.5" with the dog bones. Again, you need to verify that the tire won't touch the fender at full compression. Dropping the front as much as possible will help keep the bike balanced, and assist with the lowering. Again, you need to pull the fork spring out, and only drop the front until the tire still has space under the fender. You DO NOT want the front tire to contact the fender under any circumstances. Likely something like 3/4" is possible.
Either way, you shouldn't leave the bike the way it is, and a stiffer spring alone is not the answer