Sorry if I come across a bit harsh, but I just call it how I see it. We learn from our mistakes, but we become wiser by studying where we might go wrong.
The stock valve covers should be fine, just make sure to remove the baffles if you plan on running anything other than the stock rockers.
As for an adjustable programming system, I strongly advise you to spend your money elsewhere. These things have a steep learning curve and could cost you more than just your initial investment. This whole 'tuning' issue has only been a hot issue for maybe 5 years, I've been playing with Mustangs since I was 15 in '95 and have never had an adjustable tuning system. Between myself and my friends, we have owned so many Stangs with every conceivable combination and many of us ran un-tuned stock EFI systems without issue. Though I must admit, having just re-read the thread, I don't know the mods on your car so maybe you'd like to enlighten us?
SS

 

Hehehe well no harsher than me at first. But yes the stock valve covers are fine as far as functional minus the baffles. I'm running comp cams roller rockers 1.6's I just wanted something nicer looking. As far as other mods i don't really know where to start. Engine wise there is stock bottom end and that's about it. It has girdle and all arp fasteners though to help it stay as a single unit. top end, well, aluminum heads, e303 cam, all reworked for a turbo. Which is a turbonetics 60 mil. blowin through a spearco air to air , 70 mm bbk throttlebody comp cams composite intake etc. etc. Fuel system ignition etc; has all been done properly to support as well as the rest of the vehicle. Full length subfrrame ties, all frame support boxes are double plated and a six point cage, lakewood drag launch shocks and struts eibach springs and so on. There are a couple of reasons I was thinking on a tuner. One because it will have to go in for an emissions test next summer and i do know a person who has experience with tuners and he could probably get a tune set up for me lean enough to pass. Then i could go back to a little safer and more economical tune on the highway and of course have another one for the track Finally I would really like to be able to run this car on ethanol whenever possible although it can be hard to get in my area. But it would help me feel better about burning massive amounts of petroleum. So a fourth tune for that would pretty much fill the programmer. As far as a learning curve i can just imagine it could be pretty harsh but like I said i know somebody with experience plus i believe if you send Anderson your specs they'll send you a base tune to start with. Other than that I'm thinking the next purchase will be a short block probably a dart, not sure if im gonna fork the cash for aluminum though also haven't decided on 331 or 347 i always say the bigger the better but I've heard of wrist pin issues with 347s and premature wear problems so i guess that's another thing i'll have to study more. So before i write a book here that's a quick summery of the mods so far and why the programmer could be usefull for me, even just to keep the car legal.