I have re-geared my 1999 Yamaha Warrior 350 by subtracting 1 tooth from the front sprocket and adding 3 to the rear. To gain some top-end without losing too much on the bottom should I change front?

dropping one in the front and going up in the rear has lowered your overall gearing. Unless you had trouble getting to full revs before this will have lowered your available top speed. Getting faster at the top w/o losing any at the bottom is pretty much impossible, you can't really have both.