Have fun playing, and hope we share a mahjong table one day. Regards.

You seem to be mixing up the terms "menzen hand" and "menzen tsumo."

I'm not going to go individually about every yaku you posted, however wherever you say "menzen tsumo" you actually mean a "concealed hand."

A concealed hand (menzen) is a hand without any called tiles (naki). If you win a concealed hand by tsumo, your hand is fully/strongly concealed, meaning all melds (mentsu) in your hand are in fact concealed (ankan, ankou, anjun). If you win by ron, your hand is weakly concealed, meaning that all mentsu in your hand are concealed, except for the one completed by your win on discard (111m,333p,4448899s ron on 9: 111m, 333p and 444p are concealed. However, 999 is not, and for scoring purpouses it's counted as an "open set/pon" (minkou). So you wouldn't get suu an kou, but simply san an kou + toi toi for a total of 4 han points; your hand, however, is considered concealed).

Menzen tsumo (menzenchin tsumo hou) is a yaku that grants you 1 additional han, and it consists on drawing your own winning tile in a concealed hand.

Now, some yaku have a property called "kuisagari" which basically means "eat and decrease." Meaning that if they are formed by eating/calling discards, their base value is decreased by 1 han.
So, for example, Jun Chan Tai Yao (junchan), grants you always 3 han if it's concealed (tsumo or ron, doesn't matter), and 2 han if it's completed by eating discards.

So, Jun Chan Tai Yao (junchan)'s base value is 3 han if menzen/concealed hand, regardless of ron hou or tsumo hou. It's value is only decreased to 2 han if you completed it by having previously called a tile to form a mentsu.

123789m, 79p, 12399s (hand), ron on 8p: 3 han
123s(chi) - 123789m, 79p, 99s (hand), tsumo on 8p: 2 han.
123789m, 79p, 12399s (hand), tsumo on 8p: 4 han (jun chan + menzen tsumo)
123s(chi) - 123789m, 79p, 99s (hand), ron on 8p: 2 han.

Some other yaku, are "menzen," meaning they can only be completed on a closed hand. Some because of their structure, and some just because they were decided that way.
Chii toi tsu and kokushi musou must be concealed, because there is no way you can get those hands open. But you can still win on ron or tsumo regardless. Same thing happens with Suu An Kou, because if you have at least one of your mentsu open, there's no way you can comply with the specification for that yaku (four concealed sets).
ii pei kou, ryan peikou and chuuren (to mention just a few ones you posted), were just decided to be menzen (I think there is actually a pretty good reason for this), and as long as you keep your hand concealed, it doesn't matter if you win on ron or tsumo, as long as your hand is menzen/concealed.

Some other yaku, are just "Yaku" and it doesn't matter whether -the hand- is open or closed as long as the specifications of that yaku are complied (toi toi (all sets), san an kou (three concealed sets), shou san gen, etc).

At least, in the common ruleset, which is what I assume you will be wanting to use.

If you need further clarification, check here: http://www.sloperama.com/majexchange/bulletinbd-archive2.htm and scroll (or ctrl+f) all the way to the question by Marissa Vincenti. But I really hope this is clear enough.

Pinfu - Optional rule "Tsumo Pinfu" (Pinfu only on Tsumo). If not in effect, Ron Pinfu DOES count the 10 fu for menzen ron (while a tsumo pinfu's 2 fu for menzen tsumo are ignored)

Iipeikou - Menzen tsumo only

San An Kou & Suu An Kou - The KOUTSU must be concealed, not the hand. Thus, can only ron if the called tile is not part of the san an kou/suu an kou. Also, the fourth set for san an kou can be open. Suu an kou is double yakuman if waiting for pair.

Sanshoku Doujun - 2 if menzen tsumo, 1 otherwise

Ittsuu - 2 if menzen tsumo, 1 otherwise

Chanta - 2 if menzen tsumo, 1 otherwise

Chiitoitsu - Menzen tsumo only

Honitsu - 3 if menzen tsumo, 2 otherwise

Junchan - 3 if menzen tsumo, 2 otherwise

Ryanpeikou - Menzen tsumo only

Chinitsu - 6 if menzen tsumo, 5 otherwise

Chuuren Pooto - Menzen tsumo only (optional rule allows for menzen ron). Double yakuman on 9-sided wait.

Kokushi Musou - Can ron regardless of wait. Double yakuman if 13-sided wait.

Fixed, uploaded. TACOS already said thanks, so I don't have to.

...
thanks.

San Shoku Dou Kou is 2 han, yaku. San Shoku Dou Jun is 2 han closed, 1 han open, kuisagari. No exceptions.