I just replaced all the insides of my toilet, now when I flush I have to hold the handle down until all the water runs out of the bowl. If not almost as soon as I let the handle go the flapper will cover up the hole that drains the water into the bowl. I know this is easily fixable, but I don't know how.

Thanks for any help

With the tank full and the flapper seated, the linkage wants to have 1/4" of play. Too much play and the flapper gets pulled back
And then sucked down giving you a short flush. Too tight and it lets water seep past the flapper. I adjust the chain by the link and if it needs fine tuning, I bend the flush lever rod a bit until I have the desired linkage. Good luck Tom