1)The number of intel entries is limited?
Yes, species.tbl can have a maximum of 30 entries. Any more than that will just be ignored. It will be made dynamic with the new pilot file code however.
The Species has a dimensions limit?
Not sure exactly what you are referring to there. If you mean the actual number of species, in species_defs.tbl, then no, there is no limit for that. Or, not now at least. It was made dynamic a few months ago, but the previous limit was 8, I think.
You can have as many as 10 $bayXX paths on a model, though I'd like a significant boost to this, to support the path restriction capabilities added to FRED.
It will undoubtedly be made dynamic post-3.6.9. Most every limit that currently exists will go dynamic by the time 3.7 gets here.