BS”D
1) Sometimes the fault of poor integration lies with the BT himself. I cannot tell you how many I know who still follow various treyfe music or who are into all kinds of New Age garbage. Unfortunately there is no one like Rav Avigdor Miller ZTL or R’ Eli Teitelbaum ZL now who is able to deliver toichecho and break through such klipa beahavas Yisroel.
On the other hand, some BT’s who are not conformist are best advised to go to perfectly halachic “alternative” communities like Breslov where they fit in better and are able to live according to Torah but in their own culture. Nothing wrong with that at all.
2) We need more schools. Plain and simple.
3) Everyone has documentation of some sort in the modern world and it is usually enough to prove there is no mamzerus. Issues regarding conversion usually come out and once it does, the sincere BT is willing to do gerus whereas someone who is not as strong simply drops out at that point. The problem of conversion affects perhaps 5% of potential baalei tshuva, if that. Most products of such conversions could care less about Judaism or are so steeped in the movement that converted their mothers that they would never look at Torah and in this case we can only say B”H.
We cannot leave a single Jew behind. We are leaving 90% of Jews behind. And if we don’t act, Deformed is only too happy to get a few more members for its tembels by offering some feel good program.