Does anyone a list of primitives that are kanji in their own right, but never given a number by Heisig? Things like the long-tailed-monkey 禺, three-legged-crock 鬲, and "rice seedling" mushroom 圥?

That depends on how you classify a Han character as being kanji; none of them are supposedly on the jōyō kanji list, so anything goes. Anyway, I have a partial list of Han characters that are mentioned as primitives in RTK1&3—some have numbers in RTK3—that I paired with the JIS X codes (Japanese Industrial Standards: kanji/character sets) and definitions of an older version of Unihan, which maybe can give you some direction. Here it is—no Heisig's primitive names given for obvious reasons:

丿 (JIS X 0208-1990: 4808) line; KangXi radical 4
丨 (JIS X 0212-1990: 1609) (same as 〡 HANGZHOU NUMERAL ONE 〡) number one; line; KangXi radical 2
勹 (JIS X 0208-1990: 5017) wrap; KangXi radical 20
畐 (JIS X 0212-1990: 4521) to fill; a foll of cloth
冂 (JIS X 0208-1990: 4936) wide; KangXi radical 13
宀 (JIS X 0208-1990: 5363) roof; KangXi radical 40
辶 (JIS X 0212-1990: 6520) walk; walking; KangXi radical 162
夂 (JIS X 0208-1990: 5273) go; KangXi radical 34
冖 (JIS X 0208-1990: 4944) cover; KangXi radical 14
亠 (JIS X 0208-1990: 4821) head; KangXi radical 8
亢 (JIS X 0208-1990: 4822) high, proud; violent, excessive; skilled; name
攵 (JIS X 0208-1990: 5830) rap, tap; radical number 66
弋 (JIS X 0208-1990: 5521) catch, arrest; shoot with bow
戊 (JIS X 0208-1990: 4274) 5th heavenly stem
戌 (JIS X 0208-1990: 5692) 11th terrestrial branch
廴 (JIS X 0208-1990: 5514) go; KangXi radical 54
聿 (JIS X 0208-1990: 7070) writing brush, pencil; thereupon
冂 (JIS X 0208-1990: 4936) wide; KangXi radical 13
冫 (JIS X 0208-1990: 4950) ice; KangXi radical 15
啇 (JIS X 0212-1990: 2155) to stalk; the stem; the foot; the base
咅 (JIS X 0212-1990: 2103) to spit out
豕 (JIS X 0208-1990: 7621) a pig, boar; KangXi radical 152
隹 (JIS X 0208-1990: 8018) bird; KangXi radical 172
囗 (JIS X 0208-1990: 5188) erect, proud; upright; bald
扌 (JIS X 0212-1990: 3123) hand; radical number 64
殳 (JIS X 0208-1990: 6153) name of old weapon; kill; rad. 79
云 (JIS X 0208-1990: 1730) say, speak; clouds
曷 (JIS X 0208-1990: 5911) why? what? where?
壬 (JIS X 0208-1990: 3149) 9th heavenly stem
彐 (JIS X 0212-1990: 2887) snout; KangXi radical 58
弗 (JIS X 0208-1990: 4206) not, negative
丂 (JIS X 0212-1990: 1601) obstruction of breath (qi) as it seeks release; variant of other characters
阝 (JIS X 0212-1990: 7036) place; KangXi radical 170
圣 (JIS X 0212-1990: 2315) holy, sacred
幺 (JIS X 0208-1990: 5486) one; tiny, small
卩 (JIS X 0208-1990: 5039) seal; KangXi radical 26
艮 (JIS X 0208-1990: 2617) seventh of eight diagrams
旡 (JIS X 0208-1990: 5860) choke on something eaten
乂 (JIS X 0208-1990: 4809) govern, control, manage; nurture
凵 (JIS X 0208-1990: 4965) receptacle; KangXi radical 17
夬 (JIS X 0208-1990: 5279) parted; fork; certain
疒 (JIS X 0212-1990: 4538) sick; KangXi radical 104
匚 (JIS X 0208-1990: 5025) box; KangXi radical 22
癶 (JIS X 0208-1990: 6602) legs; KangXi radical 105
彡 (JIS X 0208-1990: 5536) hair; KangXi radical 59
氐 (JIS X 0212-1990: 3841) name of an ancient tribe
甫 (JIS X 0208-1990: 4267) begin; man, father; great; a distance of ten li
釆 (JIS X 0208-1990: 4048) distinguish; KangXi radical 165
乇 (JIS X 0212-1990: 1618) to depend on, to entrust with
卜 (JIS X 0208-1990: 4346) fortune telling; prophesy
儿 (JIS X 0208-1990: 4925) son, child; KangXi radical 10
几 (JIS X 0208-1990: 4960) small table
刂 (JIS X 0212-1990: 1917) knife; radical number 18
厂 (JIS X 0208-1990: 5044) factory, workshop; radical 27
灬 (JIS X 0212-1990: 4136) fire; radical number 86
莫 (JIS X 0208-1990: 3992) do not, is not, can not; negative
犭 (JIS X 0212-1990: 4277) dog; radical number 94
衤 (JIS X 0212-1990: 6019) clothes; radical number 145
巾 (JIS X 0208-1990: 2250) kerchief; towel; turban; KangXi radical number 50
云 (JIS X 0208-1990: 1730) say, speak; clouds
喬 (JIS X 0208-1990: 2212) tall, lofty; proud, stately
戠 (JIS X 0212-1990: 3111) a sword; potter's clay; to gather
竟 (JIS X 0208-1990: 8079) finally, after all, at last
也 (JIS X 0208-1990: 4473) also; classical final particle of strong affirmation or identity
昜 (JIS X 0208-1990: 5870) to open out, to expand; bright, glorious
广 (JIS X 0208-1990: 5488) wide, extensive, broad; rad. 53
忄 (JIS X 0212-1990: 2924) heart; radical number 61
孚 (JIS X 0208-1990: 5353) brood over eggs; have confidence
歹 (JIS X 0208-1990: 6138) bad, vicious, depraved, wicked
舛 (JIS X 0208-1990: 3304) oppose, deviate, be contrary to
曼 (JIS X 0208-1990: 5056) long, extended, vast; beautiful
彳 (JIS X 0208-1990: 5538) step with left foot; rad. no 60
禾 (JIS X 0208-1990: 1851) grain still on stalk; rice plant
从 (JIS X 0208-1990: 4826) from, by, since, whence, through
并 (JIS X 0208-1990: 5485) combine, annex; also, what's more
敝 (JIS X 0208-1990: 5841) break, destroy; broken, tattered
尸 (JIS X 0208-1990: 5389) corpse; to impersonate the dead; to preside; KangXi radical 44
礻 (JIS X 0212-1990: 4843) cult; radical number 113
乍 (JIS X 0208-1990: 3867) first time, for the first time
隶 (JIS X 0208-1990: 8016) subservient; servant; KangXi radical 171
尹 (JIS X 0208-1990: 5390) govern; oversee; director
而 (JIS X 0208-1990: 2809) and; and then; and yet; but
卉 (JIS X 0208-1990: 5035) general term for plants; myriads
尭 (JIS X 0208-1990: 2238) a legendary ancient emperor-sage
咼 (JIS X 0208-1990: 5105) chat, jaw, gossip, talk; mouth
圥 (JIS X 0212-1990: 2317) mushroom
丰 (JIS X 0212-1990: 1613) abundant, lush, bountiful, plenty
耒 (JIS X 0208-1990: 7048) handle of plow; plow; rad. 127
韋 (JIS X 0208-1990: 8074) tanned leather; surname; KangXi radical number 178
于 (JIS X 0208-1990: 4818) in, on, at; go to; surname
尞 (JIS X 0212-1990: 2675) fuel used for sacrifices
亦 (JIS X 0208-1990: 4382) also, too; likewise
巴 (JIS X 0208-1990: 3935) greatly desire, anxiously hope
其 (JIS X 0208-1990: 3422) his, her, its, their; that
丵 (JIS X 0212-1990: 1614) thick (grass)
冓 (JIS X 0208-1990: 4942) a secluded place; secret cabinet
镸 (JIS X 0212-1990: 6993) long
爰 (JIS X 0208-1990: 6409) lead on to; therefore, then
屰 (JIS X 0212-1990: 2702) disobedient
豸 (JIS X 0208-1990: 7624) KangXi radical 153; legless insects; a legendary beast
离 (JIS X 0212-1990: 4883) rare beast; strange; elegant
粦 (JIS X 0212-1990: 5118) phosphorus
夋 (JIS X 0212-1990: 2465) to dawdle; the emperor Yao's father
叕 (JIS X 0212-1990: 2060) to connect
豈 (JIS X 0208-1990: 7617) how? what?
夭 (JIS X 0208-1990: 5280) young, fresh-looking; die young
韭 (JIS X 0208-1990: 8076) scallion, leek; radical 179

Plus some characters that have definitions but no JIS X codes in the database:
丷 kwukyel
艹 grass; radical number 140
亼 to assemble. to gather together
? to cut, wound, hurt
㦮 (abbreviated form of 錢) money; cash, a unit of weight, a Chinese family name
? a roll
? to store up, to pile up
㔾 (same as 筄) last name; KangXi radical 26; a joint, a seal, (ancient form of 節)
丩 to join or connect the vine
? folded hands
堇 yellow loam; clay; season; few
尃 to state to, to announce
丬 half of tree trunk; rad. no. 90
复 return; repeat; repeatedly
兑 cash; exchange
开 open; initiate, begin, start
㕣 a marsh at the foot of the hills, (interchangeable 湢, 沇)name of a river
亻 radical number 9
耂 variant of radical 125
夹 be wedged or inserted between
夗 to turn over when asleep
亲 relatives, parents; intimate the hazel nut or filbert tree a thorny tree
㐮 (same as 襄) to help; to assist, to achieve, to rise; to raise
覀 variant of radical 146
亚 Asia; second
䍃 a vase, a pitcher, earthenware
关 frontier pass; close; relation

It's not a perfect list because at the time I made it I had no idea of what I could do to search for and add uncommon components that are part of kanji in a reasonable way, so there's a great deal of manual work involved (now I do have a better way, but I still haven't updated the list.)

Thanks. That's very informative.

My goal in asking was to figure out what obscure bonus kanji I might have picked up along the course of doing Heisig. I already know how to write things like 圥 so might as well give them a keyword and have a few more characters in my repertoire. However you raise a very good point about the ambiguity in which Han characters are kanji and which aren't, so I should probably just add such things to SRS only if I see them in the wild.