Well first off recognize that your goals are lofty.
I'm sure you've realized this, but I wanted to emphasize it. Holdsworth is an absolutely batshit player.
Still, were I working on your goal, there are some things I'd try. For modes, there are some standard chord-mode relationships. People give it over-complicated names like Pitch Axis Theory or might just call it chord-scale relationships. I'm not super familiar with them. But an Emaj7 chord would allow you to play E Mixolydian or something. I can't remember this, but someone else will probably post it, it's been posted in the forum (in the Jazz/Acoustic section, I think), so do a search for modes.
Aside from that, you may wish to develop a Holdsworthian approach to scales. This doesn't require you to learn frightening scales, but is a way to look at any scale. He views them as a collection of intervals, which he "sees" all over the entire neck
. Then with each different chord, he sees a different scale to correspond to it. As a bonus, he doesn't think modally, but rather sees scales as interval permutations from which he can select different notes.
For chord tones, once you can see them, you have a lot of options of applications. The obvious is to either hit them at the beginning or end of phrases or to hit them a few times throughout phrases. Arpeggios are another choice, but you'll want to avoid endless torrents of them. Aside from arpeggios, you can approach the chord either from scale tones or chromatically.
Approaching from a half step is common in jazz (though I'm thinking more of a rhythm guitar approach, it might be worth messing around with). In the context of jazz, you can play a chord within
the chord. My meaning: jazz has big chords with tons of notes. A G13 chord has seven tones if fully fleshed out, G B D F A C E. You could play G major, but you could also play Bdim or A minor. You could also take a polychord approach (think Romantic-era classical music) and play an A minor arpeggio over an E minor chord. I know that this example could also be though of as a minor 6th chord or something, but it's a different way of thinking and can yield different results.
EDIT: You could also work on crafting really odd angular lines by playing tones from those big chords that are relatively far apart. It might work, but no one will know why.
Yeah, for chord shapes you might want to spend some time and work out some that sound good (but don't fear really difficult fingerings; Holdsworth is not afraid!) to you. Then spend time getting them under your fingers. Then, once you have a few under your belt, take a fake book and work through it. Don't worry about getting it all at once or playing at whatever tempo. You're going for crazy skill so let it take a while.
Realize though that what chords you select will be influenced by with what or whom you play. Jazz cats comping with a piano player often play only the third and seventh of chords because the keys are so harmonically busy. If you have a bassist, you won't need to play the root-- either at all or as the lowest note of the chord, depending on what you're going for.
For other challenges, dip your fingers into chord-melody playing. Usually this involves playing a chord and then a few notes, but also dig the block chord solos of Wes Montgomery.
This probably seems overwhelming now
. But get together a quick practice schedule. 10 minutes on modes and scales, 10 on chord-scale relationships, and 10 on chords. Dig in a little bit at a time, set small
goals. Shit, if you get together a some chording skills, can play a little modal stuff, can see over the whole neck or big sections of it (not chained to the "boxes"), and can hit a few chord tones tastefully, then that's a pretty big accomplishment.