There are 4 things fixed that concern BGR. Install the
fixes for 6.3 specific bugs, and
another here which removes supplies from agents-early era only and install the 2 fixes for BGR bugs at the top of
this thread
I'm not sure because I only wrote BGR, I didn't integrate it into 6.3. However, normally with BGR if you are able to recruit knights as you say then recruitment restrictions are off for that general. The number of turns for units to become available (replenishment rate) is not controlled by BGR, but is a feature of RR mod. Also in RR when units appear is controlled by events so if you have not had the right event yet you wont get the unit.
Apart from that, if you have RR turned off then 6.3 does not work properly (it prevents some units appearing ever) unless you applied a fix and I'm not sure if that is fixed yet.
EDIT: wait-i figured out why i can't recruit. my faction zeal is verrry low.

: so, now that that is all figured out, how do i get my zeal up?
Regarding getting a warning for an attack with your WC: check your leader's traits for any orders you may have missed. There are some new orders in BGRIV_E, which are only hinted at in the instructions, but they do get announced in your faction announcements scroll so make sure you read them.
Regarding the crusading army disappearing, that would not be BGR code related if it happened in your own turn. However if you mean you retreated, as in an ai army engaged you on the map and you withdrew during the ai turn and your army was gone when you reached your own turn, then that would be BGR or crusade related. Your army deserted. You probably have low loyalty and/or low King's authority and you retreated, possibly leaving supplies behind, but certainly affecting morale. Movement away from your target whilst on crusade is also bad.