I'd personally like to see a "strike" command where you can hit world objects like walls with your weapon. Would make breaking walls and doors down a lot simpler than having to find a decent wand or training LStr.

A very basic rule of IVAN which many first-time players tend to miss is this:
This is not a nice game. You are not "the lone marine who brings down hell's legion". You are not an unbeatable Spartan warrior. You are just an ordinary guy and you are weak.
And that means a gung-ho attitude and "bravery" will get you killed.
Do not be afraid to run!
Use your head!
Make sure to progressively upgrade your equipment!

A scroll of harden material or change material or golem creation should work.

I think should you need to remove said limbs, traps are actually effective with the right preparations.
I think most importantly in the case of amethyst limbs, you would need to reduce their health down to red through fighting with monsters to make sure they come off easily. This is easily achieved if you have quite a few healing potions on you because they don't heal artificial limbs and will still heal your torso, head and groin.

Next you should probably find a very strong belt, helmet and body armor set. Having a wand of teleport or scroll will be very useful if you screw something up really bad with a bear trap. So, to remove the legs find a bear trap made of a very strong material (adamant maybe?) and remove your boots. Step into the bear trap and just mash directional buttons until the trap either breaks or the limb comes off. Now there are a few problems with bear traps, the biggest probably being getting your head caught as BDR said. That is where the scroll or wand of teleport comes in. Assuming you haven't got both your arms stuck of course, (not sure if this affects reading a scroll though). Also something big might just come along and start eating you while you're helpless so try to do this in a room where you have a key to lock the door(s).
Arms are a lot harder to remove, but with some luck you could try removing them by getting them stuck in a bear trap while trying to escape. An easier way would be mines. Have high END and/or some really powerful armor (but not fire resistance!), remove your gauntlets and just walk around the dwarven mine field for a while.
Also this should go without saying, but make sure you have the means to restore your limbs beforehand!
But as BDR said all this is really quite risky, so be careful when trying it!

Hmm... I dunno. I think the random stats at the start adds a kind of uniqueness to each playthrough. Like if you started with high DEX and AGI and they went up quite quickly, then you could afford to wear the heavy armor types like plate mail and metal boots, as well as being quite deadly with inaccurate weapons. And if you had high learning speeds for INT and WIS you could potentially gain some very nice artificial limbs as the game went on (much faster than the typical character who would have to grind through books and science talk to get to the next INT milestone).
Also it allows you to choose to build on your strengths or cover your weaknesses.

Having all your limbs amethyst really causes more problems than it's worth. For one, because of the extreme lack of flexibility your DEX and AGI will be horribly low, whilst your LStr and AStr will be very high, as well as limb health.
The problem is this: you will have a very low chance of dodging let alone landing a blow (although should you do so it will be devastating!), and although your limbs will be able to survive many hits it is important to remember that your other body parts cannot be changed. That means that all your vital body parts remain with very little HP, and if you remember that your torso takes the most damage on average, that means that not being able to dodge an attack will lead to a quick death.

My strategy for artificial limbs is this:
Should you encounter a SoCM and want to use it for changing a limb, generally the best materials to choose from are from the cloth/leather branch.
This would be, in order of scroll of harden material ranks: Leather, [Nymph Hair], Hardened Leather, Troll Hide, Ommel Hair, Phoenix Feather, Dragon Hide.
The best over all is Golden Eagle Feather, but that cannot be obtained through harden material scrolls. Note that as you go up the ranks each requires a higher INT to harden.
My advice to you is that if you should encounter a SoCM very early in the game (e.g. in the underwater tunnel) the first material you should transform your limb into is troll hide, and then later harden it to ommel hair which is only difficult if you didn't start with 10 INT or more. From there you need to read, pray and science talk to boost your INT to 20 in order to harder your limb(s) to Phoenix Feather. Phoenix Feather is very strong in both strength and speed, for example in one run through the game I had a character with two Phoenix Feather arms and he plowed through everything that came at him (including the shop guards and shop keeper in the gloomy cave AND most of the dwarven city populous in LIVAN) but was finally taken down by a couple of veteran kamikaze dwarves.
And that is the final danger of artificial limbs: They raise the danger level to the point that very strong monsters will come at you earlier than they would normally, and you are likely not to have good enough equipment to withstand them. So it is important to monitor your equipment and adjust your limbs accordingly. In short, if you are still wearing iron boots and an ommel hair armor piece, don't go power hungry and turn your limbs to dragon hide.

A torso is lying here. He does not care about you.

I've never had the game crash in Mondedr in LIVAN.
Also should my memory serve me well, the mushroom is on level 12 of the gloomy cave, and few people manage to make it that far
My advice for that level is to use haste, and find the mushroom fast. The place is almost maze-like too.
Also you have to go past that damned farmer's level on the way there.
And the Enner Beast.
And probably a mystic dark frog or two.

Well, there's a plethora of new items added, plus the dwarven city in the gloomy caves, another town on the world map named Mondedr if my spelling is correct, a few more levels added to the gloomy cave, and an incredibly annoying farmer with a +10 copper axe and insane axe skill. Oh, and more boss monsters, including a gigantic carnivorous mushroom iirc.

Go SoCM your leg to something ungodly strong maybe?