"Can have multiple crafted mods" but "Item has no space for more mods"

I alt'ed my staff until it has +2 to fire gems, nothing else.
Then 2ex for Multiple crafted mods.
Nothing else. But why can't I add any mods of any type now?

it has to be rare, sounds like you are trying to multimod a blue item which only has space for two mods including the multimod. what many do is transmute and alt to get two good mods then regal then multimod

I had a thought you might be able to regal the item now (hoping for a good mod) then craft your two bench mods in so you dont waste the 2 exalt you paid

Yep, regaling works.
The usual way of doing things, as far as I know, is:
Alt-transmute until you have one/two desired mods, multimod, craft.
For +3 bows, staves there is a sure fire way that I don't fully remember.
You need a level 8 Catarina (for Staves) and a level 8 Tora for Bows (iirc).

Yes! you were totally right about the problem being it was magic not rare... and a regal did turn it rare and allow more mods:)

Now it's +2 fire gem (alt), +40 int (regal), Can have mult crafted mods, Cannot roll caster mods. Id like Cannot roll attack mods but I get "may not have another suffix mod" :/ I thought I saw that this was possible?

Basically I'm trying to get a +3 skill staff for SRS following what others have done...

There is a very precise order of operations needed to get a +3 staff (see this reddit thread, ignore the prices though because this was written during late Harbinger), and I think you made a mistake in your process. As far as I know, you're supposed to multimod it when +2 fire is the only affix. Then you craft multimod + cannot roll caster + cannot roll attack + flat mana, and then you exalt it directly because +1 gems is the only possible affix remaining at this point (don't forget to craft mana! otherwise you could exalt flat mana and feel terrible about it).
To do that, you want to alt-spam it until +2 fire is the only affix, then regal (making it a 2-props rare staff), then annul and hope it removes the junk affix. If it removes +2 fire, scour and try again.

So how to fix your staff, then ? You could dyill try to annul but the chances of failure are much higher when you do it after having crafted so many affixes. And if it remvoes one of key affixes, then your only choice will be to scour and start from scratch again which will be pretty frustrating. You could also craft mana and yolo-exalt, but I think the most likely result of doing this would be to brick the item for good.

Edit : in case it wasn't super clear, the reason you can't multimod "cannot roll attack mods" right now is because it's a suffix, and +40 Intelligence is also a suffix.

Totally makes sense. Yes the annulment was the missing piece to this... Hopefully it'll get rid of the +40 int and then I think the rest of the recipe will work!
Need annul first or I'd do it now and post the result...