Albini has always used custom made amps I believe. He also used metal picks and thick strings. Treble all the way up, bass all the way down. Nastiest distortion pedal you have should work. I think there's an interview where Steve talks more in depth about that stuff. You could always put a metal coathanger under your strings and play it.
As for Magic Band, this was all over the place, really, they switched gear a lot... I'd just suggest watching some of their videos, the ICE CREAM FOR CROW music video, and the live performance on youtube with the song SAFE AS MILK/BAT CHAIN/BEST BATCH YET/etc. That shows their gear pretty clear. I know they played clean, with treble ALL THE WAY UP on Trout Mask, treble at an ear piercing highness.. Really, nothing too crazy or technical about the
tone of their sound, a clean Fender Strat (used through various members and albums; 1966 model preferrably) sounds good, they usually played in open tunings, of course, OPEN D a lot..
Slack key tunings used on our set were "open G," "Open A," "Open E," and these are all tunings that result in open chords: G, A, and E major respectively. Other tunings were standard and "dropped D" which is a standard tuning except for the fact that the sixth string (the fat one at the top) is lowered one full step from E to D. (I believe this is used in Big-Eyed Beans).
All kinds of pics at beefheart.com, Gary Lucas live videos are good to watch too. Here's a random pic...
The Captain’s 10 Commandments for Guitarists
1. LISTEN TO THE BIRDS
That’s where all the music comes from. Birds know everything about how it should sound and where that sound should come from. And watch hummingbirds. They fly really fast, but a lot of times they aren’t going anywhere.
2. YOUR GUITAR IS NOT REALLY A GUITAR
Your guitar is a divining rod. Use it to find spirits in the other world and bring them over. A guitar is also a fishing rod. If you’re good, you’ll land a big one.
3. PRACTICE IN FRONT OF A BUSH
Wait until the moon is out, then go outside, eat a multi-grained bread and play your guitar to a bush. If the bush doesn’t shake, eat another piece of bread.
4. WALK WITH THE DEVIL
Old delta blues players referred to amplifiers as the “devil box.” And they were right. You have to be an equal opportunity employer in terms of who you’re bringing over from the other side. Electricity attracts demons and devils. Other instruments attract other spirits. An acoustic guitar attracts Casper. A mandolin attracts Wendy. But an electric guitar attracts Beelzebub.
5. IF YOU’RE GUILTY OF THINKING, YOU’RE OUT
If your brain is part of the process, you’re missing it. You should play like a drowning man, struggling to reach shore. If you can trap that feeling, then you have something that is fur bearing.
6. NEVER POINT YOUR GUITAR AT ANYONE
Your instrument has more power than lightning. Just hit a big chord, then run outside to hear it. But make sure you are not standing in an open field.
7. ALWAYS CARRY YOUR CHURCH KEY
You must carry your key and use it when called upon. That’s your part of the bargain. Like One String Sam. He was a Detroit street musician in the fifties who played a homemade instrument. His song “I Need A Hundred Dollars” is warm pie. Another church key holder is Hubert Sumlin, Howlin’ Wolf’s guitar player. He just stands there like the Statue of Liberty making you want to look up her dress to see how he’s doing it.
8. DON’T WIPE THE SWEAT OFF YOUR INSTRUMENT
You need that stink on there. Then you have to get that stink onto your music.
9. KEEP YOUR GUITAR IN A DARK PLACE
When you’re not playing your guitar, cover it and keep it in a dark place. If you don’t play your guitar for more than a day, be sure to put a saucer of water in with it.
10. YOU GOTTA HAVE A HOOD FOR YOUR ENGINE
Wear a hat when you play and keep that hat on. A hat is a pressure cooker. If you have a roof on your house the hot air can’t escape. Even a lima bean has to have a wet paper towel around it to make it grow.