Our cars have very similar mods. 95 Vert, AODE, Cobra intake, Cold air, full exhaust... Mine also had very similar issues idle, timing, etc. I was able to do all the basic stuff, but it was still not running right... What really helped was a chip / tune. I am now a believer. Some will say you don't really need a tune with just an intake, but I will praise the abilities of a good tune forever now...
Pre-tune dyno, it was putting down 177rwhp, post-tune it laid down 204rwhp (I know it's not much, but +27 rwhp was very noticeable for me). When the tune was over it was like night and day. The idle issues were fixed (still a slight hang, but 80% better), the car isn't running rich, my tuner modified the shifting, and I couldn't be happier. The car is way more snappy, feels overall better across the rpm range, no more popping, shifts are very crisp, and I just can't say enough about the tune. Like I said, I am now a believer. Worth every penny!!!
Should you decide to tune, find a tuner in your area that has dealt with sn95 5.0's though... they are a different animal than fox 5.0's and it took me awhile to find the right guy, but I am glad I waited.
The grin on my face driving home post-tune was priceless... Next up for me is fuel pump and finish my nitrous install and re-tune!
Good luck!