The final grid looks like this:
The four kinds of clue, less obscurely described, are:
ONE CLUE (lonely): These are clued normally, but have one or more double letters in the answer which on entry into the grid are collapsed into single letters.
TWO CLUE (twins with identity crisis): These are "double-wordplay" clues, consisting of two wordplay parts with no definition. The definition is one of the extra words from a Red Clue.
RED CLUE (communists sharing parts): These are clued normally, except that the first and last words of the clue are not used by the clue itself but form definition parts for Two Clues and Blue Clues (one of each for each Red Clue).
BLUE CLUE (sad, don't do anything twice): These are normal cryptic clues, but once the answer is found it (1) has all duplicate letters suppressed and (2) is anagrammed to form a new word, whose definition is one of the extra words from a Red Clue.
The extra gimmick is that
since this is a fish, the crossword obeys the principle that "F is H", and in some places in clues and solutions one may actually signify the other. There are only two places where there is actually any doubt which should be entered in the grid, for a reason to be described in a moment.
Three of them are resolved by
the fact that across the middle of the fish we can read FISH OUT OF WATER. (This has no particular significance other than fun.)
So here are the clues and their solutions. They are marked "1", "2", "R" or "B" with the obvious significance. Indications of who solved each clue are necessarily imprecise since they were discussed in TSL chat and some clues were solved in multiple stages for reasons that will be apparent if you have read the spoilered text above. Dan Russell was the first person to attack this, and he solved lots of early clues. Later on, it was mostly Gareth McCaughan and Volatility. This writeup is almost all by Gareth McCaughan, except that many of the individual clue solutions due to other people were written by them (though Gareth has unified the presentation somewhat for consistency).
2 Thief reboot bombs: "generic", "regular"
1 ROBBER (thief; letters appear regularly in RebOotBomBsgEneRic) entered as ROBER @Gareth
7 Florida city's third note to French friend
B MIAMI (do-re-MI + Ami) entered as MIA (def "gone" from 4d) @Dan
10 Head of Syria is equally miserable
B ASSAD "As sad" entered as ADS (def "commercials" from 1d) @Dan
12 Hate after energy carrier's symbolic gift
2 AT PRESENT (def "now" from 38a; ATP RESENT and AT PRESENT with AT denoting the "symbolic" @) @Volatility
14 Packaging game system in with candies? That's generosity
B SWEETNESS (SWEETS with NES inside; def=generosity) entered as NEWTS (def "lizards" from 24d) @Volatility
15 Edgy Bond movie about ancient, gen-I, writer
R GOLDENEYE (Bond movie; GEN EYE around OLD; "edgy"->22d, "writer"->16d) @Gareth
18 Returned donated change, heartlessly halved
2 SPIT (def "disrespect" from 21a; donated change=TIPS, returned → SPIT; halved=SPLIT but heartlessly → SPIT) @Volatility
21 Disrespect earlier half of country's sacrifice, I scream
R COSTA ("earlier half of country" is straight def, confirmed by Deusovi in chat; COST + A; "disrespect"->18a, "scream"->26a) @Gareth
24 Skins left the rest
1 SLEEP (skins=PEELS, left → SLEEP; rest=def) entered as SLEP @Volatility
26 Get away before salesman conflict
B SHOOTOUT (SHOO TOUT) entered as SHOUT (def "scream" from 21a) @Gareth
27 Latin and revolutionary quartet surround a meeting
B TETE A TETE (ET backwards four times around A) entered as ATE (def "consumed" from 3d) @Gareth
29 Going over part of poetic meter is pedestrian
1 ON FOOT (ON + FOOT) entered as ONFOT @Rubio
30 Theresa delights, swallowing fifty tiles
B TESSELLATES (TESS + EL(L)LATES) entered as TESLA (def "inventor" from 38a) @Volatility
31 Cool guy father made to sound like a tool
B DOODAD (sounds like DUDE + DAD) entered as ADO (def "trouble" from 38d) @kayzeroshort
32 Block ringer for strength trainer
1 BARBELL (BAR+BELL) entered as BARBEL @Gareth
33 Dog hugging M. P. referee
2 PUMP (def "pusher" from 3d; M in PUP, and P + UMP. The "M" and "P" are separate!) @Volatility
34 "Nice, 150 with two rings!"
1 COOL (150 = CL, two rings = OO) entered as COL @Dan
35 "Cart isn't right? Runs in reverse?" Pointless junk mail returned
2 MAP (def "guide" from 9d; PRAM without the R ("isn't right") backwards, SPAM without the S ("Pointless") backwards) @Volatility
36 Scrambled sonar hidden in guitar song
2 ARSON (def "crime" from 28d; anag of SONAR; guitAR SONg) @Dan
38 Inventor psycho I liked had a counterpart now
R FOIL (FOIL=counterpart; HOIL HOIL embedded in "psycho I liked"; remember "F is H"; "inventor"->30a, "now"->12a) @Gareth
39 Most beautiful? No, that's not right - most jealous
1 PETTIEST (PRETTIEST minus R) entered as PETIEST @Gareth
40 Help to destroy stasis
1 ASSIST (anagram of STASIS) entered as ASIST @Gareth
1 Peace changed armed fronts' repulsive commercials
R TRANSFORMED (anagram of "armed fronts"; "peace"->5d, "commercials"->10a) @Volatility
2 Storefront, in repeated task, put up text again for the audience
2 RIPOSTE (def "backtalk" from 4d; POS = point-of-sale inside RITE, a repeated religious task; sounds-like REPOST = put up text again) @Gareth
3 Consumed some swine with wooden blade pusher
R OAR (part of BOAR, meaning a wooden blade; "consumed"->27a, "pusher"->33a) @Volatility
4 Backtalk, farewell - missing hoe gone
R BYE ("hoe"="foe" because "F is H"; a bye is a game against an absent opponent; "backtalk"->2d, "gone"->7a) @Volatility
5 Satisfy without game? Just some letters, I fear
2 EASE (def "peace" from 1d; APPEASE without APP (some apps are games and some games are apps...) and sounds like "Es" (fear = hear because "F is H")) @Gareth and @Volatility
6 "Programmer without borders" from Tokyo back in the olden days
2 ODE (def "song" from 24d; cODEr and EDO backwards) @Gareth
8 Importantly, outside, none excited Edd
B NEEDED (outsides of NonE, ExciteD, EdD) entered as DEN (def "home" from 9d) @Gareth and @Volatility
9 Guide glitchy Neo home
R ONE (glitchy Neo; &lit, anag. and def; "guide"->35a, "home" ->8d) @Gareth and @Volatility
11 Ocean's desire for hissing god
R SWISH (S+WISH; "ocean"->37d, "god"->20d) @Gareth
12 So, about Cats: both ways are abrupt?
B STACCATO (SO around TAC and CAT -- "cats both ways") entered as ASCOT (def "tie" from 28d) @Volatility
13 Toy spread oddly in center of empty pedestal
2 TYPED (def "input" from 38d; ToYsPrEaD (odd letters) = TYPED, and empTY PEDestal) @Dan
16 Boy sent north to get figurehead -- large
2 DAHL (def "writer" from 15a; LAD upward with F inside plus "F is H"; and DAH L where the DAH is Morse and comes from the dash in the clue!) @Gareth but @Deusovi had to give us a big shove for the second half.
17 Accept N→Z→N perhaps?
1 ENROLL (EN ROLL!) entered as ENROL @Gareth
19 Throw funeral cloth away for the Reverend - a game where you fit things into a hole, perhaps
1 PINBALL (Spoonerism for BIN PALL) entered as PINBAL @Volatility
20 Tea for detailed point
2 THOR (def "god" from 11d; T+FOR; THORN de-tailed; remember "F is H") @Gareth
22 Auditor moved back of garden to front, leading to pain
B (TORTURE, "garden" -> ORCHARD, "back to front" -> DORCHAR, sounds like TORTURE) entered as OUTER (def "edgy" from 15a) @Volatility
23 Throw jars at drunkards
1 TOSSPOTS (TOSS+POTS) entered as TOSPOTS @Gareth
24 Lizards moved through water, mouths returning song
R SWAM (MAWS backwards; "lizards"->14a, "song"->6d) @Dan?
25 Spaniards, the best at folding very soft support for 23D perhaps
1 LAMPPOST (PP in LA MOST; drunkards may use lampposts "for support rather than for illumination") entered as LAMPOST @Gareth
28 Crime understood: technique's second half turned back, dropping unknown tie
R TACIT (TACTIC with second half reversed and C, denoting an unknown constant in mathematics, removed; "crime"->36a, "tie"->12d) @Gareth
37 Evaluates a hissing, punctuated by echoes
B ASSESSES ("a ssss" with two Es -- ECHO from the phonetic alphabet -- inserted) entered as SEA (def "ocean" from 11d) @Gareth (with nudge from Deusovi in chat)
38 Input "one" - is she broken? Trouble
R HES (one is; anag. of SHE; "input"->13d, "trouble"->31a) @Volatility