First, Welcome to ENWorld!
Yeah, the D20 Modern book (Gamemastering section) doesn't have as much help for this as the D&D DMG does (3.0 or 3.5).
For your specific example (determining the CR of a basic thug) you want pg. 271 of the D20 Modern Book. Remember that the CR of a creature/NPC equates to a moderate challenge for four PC's of the same level as the creature/NPC CR (i.e.: CR 4 creature/NPC vs. 4 PC's of level 4). CR of an ordinary NPC (made using normal NPC classes - no special abilities) is their level -1 (page 271). The book also has low-level, mid-level, and high-level versions of basic Thugs on page 273-274. To change their level and CR, I'd use the formula on pg. 102 of the 3.0 DMG (under the Tougher Monsters section), or
this section of the D20 SRD.
Some other things you can do to determine a CR, are to look for a monster that's already in the book that has the CR you want, then "reskin" it to fit the monster or NPC you envision (keep the "stats": Hit Dice, BAB, abilities, etc. - and just change the description). Or find a "base" version of what you want in the book, then increase their Hit Dice, BAB, Saves, etc. and use the D&D DMG to calculate the increased CR.
I won't reprint anything from the books here, but here are some references that might help you:
D20_Modern_SRD (at WotC website) (especially the Creature Overview, Creature Types, and Creatures sections - of course though, the D20 Modern SRD at WotC was meant to be used with the book, so it doesn't have a Gamemastering section.)
D20_SRD (the hypertext D20 srd)
D20_SRD_Advanced_Monster_Challenge_Ratings (@ the hypertext D20 srd)
Applicable parts of the books:
D20 Modern RPG book, Gamemastering section, pages 205-206, 217, 271-283
D&D 3.0 DMG, Chapter 4: Adventures, Tougher Monsters section, pg. 102. (there's a good formula there for how to increase or decrease a CR).
D&D 3.0 Monster Manual, Creature Advancement by Type chart on page 13.
D&D 3.5 DMG, Chapter 3: Adventures, Tougher Monsters section, pg, 50. (However, the formula isn't in the DMG for 3.5 - it references pg. 293 of the 3.5E Monster Manual - in the Advanced Monster Challenge Rating section.) *sorry, I don't have a 3.5E Monster Manual so I can't confirm it for you.
You might have better luck finding specific help in the
Other RPG Discussion forum. This is where the D20 Modern specific people hang out.
I hope this helps.
