I have a 87trx250x and have bored it to 76mm with wiseco 12to1. Will the stock 300ex carb work as far as jet size?  

have you tried the stock 25o carb?

you might come out better.

the 300ex carb would work but you would most likely have to jet it.  

Yes, I have two. when i tried either of these they flood the engine, I cleaned both carbs but I do not know if someone changed the jets. A friend has a 06 300ex I think I can borrow it to see how it performs.  I want to purchase a new carb. from honda and the 300ex carb is cheeper by $50.00. Just wanted a more educated opinion.  How would you know what jet to use?  

well if it is flooding the engine then chances are the jets are too big, unless the air/fuel mixture is waay off.

try the air fuel mixture screw or have you already?

turning it to the left adds more fuel, while turning it to the right reduces the amount of air and allows for more air in the mix.  

tried setting to 2 1/2 turns out and then adjust the air fuel mixture it runs but still floods.  when i try to give it the gas it dies or full throttle will rev good but alot of fuel smoke.  

sounds like you need to reduce the jets.

if you go with the 300ex carb you are going to have even larger jets.

check the needle on the 250cc carb see if it is set to it's top groove.
it should be if not.  

when I cleaned the carb I set the need clip in the top groove it was in the middle groove, the jet has 125 on it I think this is stock but couldn't they be drilled?  the parts list for the 300ex carbs lists a 122 jet. what do these #'s mean. ? Is the 122 smaller or larger?  

with what you have bored it to you shouldn't have to rejet the stock carb. but you would have to readjust the air/fuel mixture.

with the 300ex carburetor you would almost certainly have to rejet the carb to smaller jets.
you can buy a multi jet kit. where you have 4-6 different jets sizes depending on the kit you buy, and you can custom select the jets you need depending on what you need.