‘ 06 trx 350 clutch help

I’ve got a few questions here . I picked up an 06 TRX 350 , foot shift , SRA , a month ago and finally got around to doing some maintenance . Wonder if yall could help with a few questions ?
1) I changed the oil and filter and put in Castrol 10-40 synthetic , jaso was listed on the label . now it is a little hard to upshift from about 3rd gear on up . And when stopped in 1st gear , it won’t go into neutral , I have to turn the bike off , go into neutral , then start the bike . Have I screwed the bike up by just changing the oil , or does it usually have a break in period when switching to synthetic , if it wasn’t synthetic to start with ?

2) It has no front brakes , the master cylinder had fluid but looked to have water and dirt in it . Brake pads are shot . Am going to put on new pads . The wheel cylinders look to be possibly stuck in position . i took 1 off but haven’t tried messing with it yet to see what the inside condition is , but there was fairly clean fluid coming out of the brake line when I removed it .Do these cylinders seem to work properly when rebuilt , or is it better to replace them with new cylinders ?
Thanks for all your help .