as far as what works on both motors i'm not completely sure. i know the head and jug are different and the cam shaft selection i believe is more abundant for the 4 bolt. as far as clutching not 100% sure.
i prefer the 4 bolt for the parts availability. the standard gy6 w/out the internal reverse is what i use and prefer. as far as a brand of motor, i have always had luck w/ Howhits.
i would say Tom syc could give you a better rundown on the pro's and cons of 2 bolt vs. 4 bolt.
every custy motor that's been through my shop thus far has been 4 bolt just because they are more common.
as far as swapping out a whole motor via paying to having one built for you if you wouldnt do it yourself i would recommend either Tom Syc or my shop. I have had great experience w/ Tom before i opened my shop and he stands by his work. I have an in house engine tech, Jeff, who is awesome. used to manage/mechanic an NHRA drag bike team and he's one of my best friends. all i can say is there is no "good enough" in his vocabulary. it's either on the money or it doesnt go out the door. if he didnt have this attitude i wouldnt have him in my shop and i would just stick to selling parts and fab.
but w/ the buggy you have i would 1) pimp out a 150 or 2) swap a cn or cf250 in the swing arm and do some suspension mods. i started out doing stuff to my 150 and still have it, but it's good training for fabbing.
if you want to move up in motor and buggy i would keep the 150 and hunt down a project i.r.s. buggy to do a swap into.