Welcome to the site, without bashing MSD who do a decent job mostly the chip can only ever by it's nature be an all round chip, and you will get variations, every engine is different.
Without knowing your engine itself maybe someone else has made a mod you are unaware of, which is throwing the chip/fuelling out.
The quickest and cheapest way by far is get all your mods done then take and have it live mapped, it will be perfect then, each tuner likes slightly different things however, but most of the big names do a good job, msd nms to name but a few, you seem to have covered all that would normally be suggested, but a live map will find out the problem for you.
If you were planning lots more mods in the future I would seriously consider going aftermarket ecu, as I did best thing I ever did, can now get over 400 to a tank, that was with 200,937 miles on the engine, now stripped for rebuild, emissions were 0.97% CO, 137ppm at idle on a T34, with GREY injectors, off boost power was awsomely improved with live map, picks up from 1400 full boost by 2500.
tabetha