Spell Research is... a heavy mod, compatibility-wise. To put things in perspective, currently we have:

Spell Research Patch Compendium, to patch most mods - yet now up for adoption, and already out of date with Mysticism;
Spell Research JSON Patch, for a patching method saner than having to write raw scripts - but not supporting Alchemy or tricky mods like Odin/Mysticism;
Spell Research - JSON Mysticism Patch, because there's a not-undeservedly famous magic mod that's had a major update since the activity on the Compendium stopped, but is too complex for a plain JSON patch.
Spell Research - Alternate Tome Patcher, because what's the point of the song and dance of Spell Research if you can buy and loot your way to phenomenal cosmic power? Alas, it only works with the Compendium .psc patches...

So here I present to you my solution: Spell Research Synthesizer!

Current features:
1. Imports all patches from the three patch providers, combining them into one patch;
2. Resolves conflicts between multiple patches affecting the same spell/artifact/ingredient to always use the patch for the .ESP that's loaded last;
3. Optionally updates Spell Tomes to display archetype information instead of teaching the spells directly.
4. Uses Form List Manipulator to bypass Spell Research's import procedure.
5. EXPERIMENTAL: Allow gaining Archetype XP from altered tomes (configurable).

Also included in the downloads are a handful of manual patches:
College Curriculum - the spells have archetype info and are classified as Expert, but are not discoverable. Conjure Ash Guardian tome not added to SR because it also exists in Mysticism and I do not even want to guess how SR would react to two tomes for one spell.
Expanded Novice Destruction Spells For Mysticism - because I haven't seen a patch for it yet. Two versions to support the Alternate Perspective version - the patcher differentiates them automatically.
JS Immersive Tripwires SE;
Mysticism - for the Jump Spells plugin;
Oblivion - Deadric Recall is discoverable; Conjure Bone Dragon deliberately not so you'd have a reason to go down to the Forge.
Pilgrim - for the Divine Intervention spell line. Pilgrim's Intervention to Forgotten Vale has been deliberately marked as undiscoverable - I know not the consequences of sequence-breaking your way in there.
Plague - Poison Spells Mysticism Addon
Ritual - An Adamant Addon
Saints and Seducers - the Compendium patch seems to have broken FormID's for most spells;
Singularity - the Compendium patch appears to have been using the Alduin Core as a spell tome, instead of, you know, the spell tome (not that I got that far into the game, mind you.)
Sonic Blast Magic
Spell Research - Convenience Add-On - Book Transformation spell.
Storm Calling Magic - Included patch. Interaction with power version of Streak not tested - I don't know for certain if Spell Research supports powers.
Sun and Stone Atronachs - A Mysticism Addon
Wyrmstooth - Mysticism Spell Consistency Patch - same as above, though removing instead of adding spells;
NOTE: Since I no longer use SR in my own games, I will no longer update patches/make new ones. I will only maintain the patcher itself.

The following patches have been converted from the Compendium, with Cecell's permission:
converted Compendium patches:
Apocalypse
Bruma
CC Arcane Accessories
CC Arcane Archer Pack
CC Bittercup
CC Necromantic Grimoire
CC Plague of the Dead
CC The Cause
Cutting Room Floor
Hunterborn
Hunterborn - Forbidden Prey
Psijiic Teleport Spells (non-compacted version only)
Triumvirate (with fixes)
Vigilant
Wyrmstooth

Compatibility:
Spell Research Patch Compendium - Compatible. Some patches in it are broken. Disable the ESP, or don't import its spells when prompted. USE THE LOOSE FILES VERSION.
Spell Research JSON Patch - Synthesizer supports patches intended for it out of the box, making it redundant - disable the ESP, though it shouldn't do more than extend the import procedure if it runs before mine does. If it runs after... no promises on the outcomes.
Spell Research - JSON Mysticism Patch - Supports the patch out-of-the-box.
Other Spell Research Patches - I don't use them and haven't tested them. Use at your own risk, though said risk should be fairly limited as long as they don't touch the same spells as mine does.
Immersive Spell Learning - DESTified - so far, seems to work for unprocessed tomes while ignoring the ones that have been altered to no longer teach spells, as expected.

Big thanks to:
IronDusk33 - for Spell Research;
gutieashl - for the Altered Tomes Synthesis Patcher that this grew out of;
Cecell - for the Spell Research Patch Compendium;
djarb - for the JSON Patch;
Kailithnir - for the JSON Mysticism patch, and letting me use it as the base of my own, as well as technical advice;
SailingRebel over on Reddit - for helping me figure out what absurdly obvious detail I'd missed.

Permissions:
GitHub code - Do as you will, but credit me and gutieashl;
ESP & spell import script - Again, do as you will, but credit me and Kailithnir;
SRImportPlayerAliasSynth script - as a modification of IronDusk33's SpellResearchImportPlayerAlias script, falls under the restrictions in the Spell Research description. If I'm correctly interpreting the file's presence in both the Compendium and the Mysticism patch, it's allowed to be used in Spell Research patches, if I'm understanding that wrong... well, at least I'll be in trouble right along with you.