Irregular verbs: the history of the suffix “-en” in the past participle

Did more past participles use to end with -n?

Yes. In Old English, strong verbs took the "-en" suffix in order to form the past participle:

The past participle was formed using a dental suffix for class 1 and 3 weak verbs ("-ed", "-t", or "-d", depending on the verb), and "-od" for class 2 weak verbs. Strong verbs took the suffix "-en" and the appropriate stem vowel change for their strong verb class, for example "singan" - "sungen".
_{Wikibooks: Old English/Participles}

In Middle English, "-en" and "-e" were both used to make the past participle of strong verbs (in other words, "-en" was becoming less common):

The past participle of both strong and weak verbs frequently has a y prefix; the weak past participle ends in -d or -t, the strong in -e or -en. Example: (y)gonne and (y)herd.
_{Chaucer's Grammar}

(Note that the "y" prefix comes from the Old English prefix "ge-".)

Middle English was a period of drastic change, where many things in the language were simplified. This is but one of these changes. It's explained somewhat in this paper:

Middle English was a period of extensive syntactic change, and only a selection of the changes that have attracted a good deal of scholarly attention can be mentioned here. The role of language contact in shaping Middle English syntax is currently an issue of considerable debate. An influential paper here is McWhorter (2002), who argues for a large number of syntactic changes that he attributes to contact with Norse.

You mention comen, drinken, and holden. These were all past participles at one point, among other forms, according to the OED (emphasis theirs):

OE cymen, OE gecumen, OE (Northumbrian)–eME cumn- (inflected form, in prefixed forms), OE–ME cumen, OE (Northumbrian) ME–15 cummen, lOE ecymen, lOE gecuman, eME cumenn ( Ormulum), eME ȝecumen, eME hicomen, eME icumen, eME icumn, eME ikimen, eME ikumen, ME comene, ME comin, ME cominne, ME commene, ME commin, ME common, ME commun, ME commvn, ME comn, ME comun, ME comvn, ME comyn, ME coomen, ME coomyn, ME cumin, ME cummin, ME cummun, ME cumne, ME cumyn, ME cumyne, ME icomen, ME icomin, ME icommen, ME icommin, ME icomyn, ME komen, ME kumen, ME ycomen, ME ycomin, ME ycommen, ME–15 commen, ME–15 commyn, ME–16 comen, 15 coommne, 15 cummyn, 15–16 com'n, 15–16 comne; Eng. regional 18 cummen (Northumberland), 18 cummun (Cheshire), 18–19 comen (Yorks. and Shropshire); Welsh English 19– cummun (Flintshire); Sc. pre-17 commen, pre-17 commyn, pre-17 comyn, pre-17 cumene, pre-17 cumine, pre-17 cuming, pre-17 cummen, pre-17 cummin, pre-17 cumming, pre-17 cummyn, pre-17 cummyne, pre-17 cummyng, pre-17 cumyn, pre-17 cumyne, pre-17 cwmin, pre-17 cwming, pre-17 18 cumen, pre-17 18 cumin, pre-17 19 comen, 19– comin.

OE druncen, ME– drunken, (ME Orm. drunnkenn, ME–15 dronken, ME dronckyn; Sc. ME drukken, 15 drokin, 16–18 druken, drucken)

α. OE--ME ( ge)halden, ME ihalden, ME halden, -yn ( alden, etc.), ME–15 haldin, (15 Sc. haldine, haulden, 18 Sc. hadden, north. hodden).

β. ME y-, i-holden, -yn, ME– holden, (ME -in, -yn, -un, olden).

γ. OE ( ge)healden, ME ihealden, ME–15 helden.

(Note that none of these lists is complete; OED lists more forms for each.)

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In group 4, were the past participles of do and go ever doen and goen respectively?

I wouldn't say that they were THE past participles. Again, spelling was not very standardized, so A past participle would be most correct. Note that both verbs are irregular (and have always been irregular in English).

Here's part of the list for past participles for these words from the OED (emphasis theirs):

OE gedoan (Mercian), OE gedoen (Anglian), OE gedonn- (inflected form), OE gedoon (rare), OE gidoen (Northumbrian), OE godon (probably transmission error), OE (chiefly Anglian) ME–15 doen, OE (rare) ME–16 don, OE–eME gedon, eME dom (transmission error), eME ȝedon, eME geydon, eME gie-don, ME dooun, ME doun, ME doune, ME doyen, ME doyn (chiefly north.), ME dun (north.), ME dune (north.), ME hi-don, ME idon, ME i-don, ME i don, ME idone, ME i-done, ME idoon, ME i-doon, ME i doon, ME idoone, ME ydon, ME y-don, ME y don, ME ydone, ME y-done, ME y done, ME y-donne, ME ydoon, ME y-doon, ME y doon, ME y-doyne, ME–15 down, ME–15 downe, ME (chiefly north.)–15 (Westmorland) doyne, ME–16 donn, ME–16 donne, ME–16 doone, ME–16 (17– regional and nonstandard) doon, ME– done, lME edoone, 15 dooen, 15 i-doen (arch.), 15–16 don't (with personal pronoun affixed); Eng. regional 16 deaun (Yorks.), 18 den (Lancs.), 18 din (Devon), 18– deean (north.), 18– deen (Northumberland), 18– deeun(Northumberland), 18– deughn (Northumberland), 18– deun (north.), 18– diun (Northumberland), 18– doin (Yorks.), 18– duin (north.), 18– dun (north. and north midl.), 18– dyeun (north.), 18– dyun (Northumberland), 19– a-done (south.); Sc. pre-17 deun, pre-17 doen, pre-17 doin, pre-17 donne, pre-17 doon, pre-17 doone, pre-17 doun, pre-17 doune, pre-17 dovnne, pre-17 dowin, pre-17 down, pre-17 downe, pre-17 downne, pre-17 doyn, pre-17 doyne, pre-17 dwin, pre-17 dwne, pre-17 dwyne, pre-17 17– done, pre-17 18– dune, pre-17 19– don, 17 dene, 17– deen, 18 deune, 18 dön (Shetland), 18– daen, 18– dane, 18– duin, 18– düne (chiefly Shetland), 19– dain, 19– din; also Irish English (north.) 19– daen, 19– din.

OE gegan, OE gen (in prefixed forms (not ge-), rare), OE (rare)—eME gæn (in prefixed forms (not ge-)), OE—ME gan, eME ȝegan, eME gun, ME gain(north.), ME gane, ME geen (in representations of northern speech), ME gone, ME gonne, ME goone, ME goyn (north.), ME igan, ME igon, ME igone, ME igoon, ME jgon, ME ygan, ME ygoen, ME ygon, ME ygone, ME ygoon, ME—15 goen, ME—16 goon, ME—17 gon, lME gonn (in a late copy), 15 i goen (arch.), 16 gaene, 16 ygone (arch.), 19— gawn (regional and nonstandard), 19— gorn (regional and nonstandard); Eng. regional 16 18— gane (north.), 16 18— gean(north.), 17 guone (Somerset), 18 gaan (north.), 18 gain (Yorks.), 18 gayn (Westmorland), 18 geyan (Lancs.), 18 gwon (Northants. and Somerset), 18 gyan(Cumberland), 18— gaen (north.), 18— gaine (Yorks.), 18— geean (Yorks.), 18— geyen (Northumberland), 18— geyn (Northumberland), 18— gi'en (Durham), 18— goan, 18— gooan (Somerset), 18— goon, 18— gwone (west.), 18— gwun (west midl.), 18— gyen (Northumberland), 19— a-gone (Berks.), 19— gan (north.), 19— gæan (Lancs.), 19— geayne (Yorks.), 19— gian (Yorks.), 19— gon; U.S. regional 18 gown; Sc. pre-17 gaan, pre-17 gain, pre-17 gaine, pre-17 gayn, pre-17 gein (east.), pre-17 geine (east.), pre-17 goyn, pre-17 ygone, pre-17 17— gaen, pre-17 17— gane, pre-17 17— gon, pre-17 17— gone, pre-17 18 gayne, pre-17 18— gan, 18 geane (south.), 18— geen (north-east. and Orkney), 18— gin, 19— gaun, 19— gean, 19— gien; also Irish English (north.) 19— gane.

(Again, there's actually more forms than just these, but you get the point.)

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Did been and seen use to have two syllables? Was it ever pronounced "be•en" and "se•en"?

I don't know the whole history. In the 1848 book A Critical Pronouncing Dictionary, and Expositor of the English Language, been and seen are both listed as having one syllable.