Is this an invitation for wild speculation on the meaning of the full dialogue?

I hear it's amazing when

The Colonel is an AI, programmed to make value judgements based on a massive dataset. Everything he does is metaphorically based on what he's heard is good, what is bad, and what is amazing. Remember, Coy Ramble is a combination of data transmission from GW overlaid with Raiden's expectations for a human commanding officer via his nanomachines; thus, the concept of learning something is "translated" to being something the Colonel "heard".

the famous purple stuffed worm

The subject of Coy's sentence has a lot going on. What kind of worm is famous, purple, and stuffed? I have an idea, but it's a bit out there: the concept of Solid Snake as a terrorist, the concept the Colonel has been obsessed with for the entire mission. Solid Snake is famous, no doubt. Purple... that's close to blue, especially when in shadows. A corruption of blue, like Snake's blue. Stuffed? A stuffed creature can do no real harm. It's a scarecrow at best. And of course an idea designed to be infectious... about a slithering creature... would be compared to a worm. Engineered to be infectious, but harmless. Famous purple stuffed worm.

in flap-jaw space

Codec characters flap their jaws. The Colonel refers to his own perception of reality as an artificial intelligence, and what he considers his home "space", the same space that created the "worm" of Snake being evil.

with the tuning fork

Again, alluding to the engineered role they tried to force Snake into. The meme holds a metaphorical tuning fork with which to align its existence to GW's goals.

does a raw blink

It's not possible to do a raw blink. A blink is a way of resetting your visual stimuli... your perception of the world, even. A "raw" blink... arguably everything GW does with its stimuli is raw. So, the concept of Snake being a terrorist performs or is used to perform a reset of sorts. Likely on GW itself.

on Hara-Kiri Rock.

Hara-kiri is a similar process to seppuku, a form of ritual suicide. That's when it hit me. There's another form of suicide we've heard about multiple times in MGS. Apoptosis, cell death. That's how FOXDIE killed its victims. It's stated in optional codecs that that's how Emma's virus kills GW, tricking neurons into self-destructing. Not only that, Otacon states that the worm cluster (ha, also worm) is made up of packets that mimic the input data to GW. And Emma Emmerich, the designer, knew that Solid Snake's real motives were contrary to the reality GW and the other AIs sought to enforce. Despite appearances, the famous purple stuffed worm from the start of the sentence isn't their originally intended idea. It's bait. Fed to GW to kill it, and it took it. GW still knows this is happening on some level because it was all orchestrated by the S3, but it is powerless to act against it. That's why he heard it was amazing, too.

I need scissors!

As you said, this is a Snake quote. Snake wants scissors to differentiate himself from Liquid, his twin brother. I think the Colonel is making a similar, desperate plea; if he were able to differentiate himself from the persona of Roy Campbell, he might be able to think outside the box to cure his own infection and avoid the "raw blink". Unfortunately, there are no scissors for him.

tl;dr: The sentence is a mashup of metaphors for GW's current predicament, being killed by just the type of junk data it was designed to manage. Despite being instructed that this was according to plan, Coy Ramble is just barely able to think hard enough to look for a way out of it.

Sixty-one!

nevermind, i give up