ok simple awnsers to most of your questions... a )you cant jump with bowser you NEVER can but he does have a body slam but thats not for these. at the point in time the red pipe in the pipe room smashes in half you can escape bowser and go into the underground seeweres in witch are right undeer toad town so anny floating boxes or special block pieces will be picked up by mario and luigi later oin in the game. also you will soon learn a dig manuver that will be used on those x marks on the ground to get beans but thats only foir mario and luigi so if you dont have dig dont worry about them.
if you ever see a place later on that has a mushy wall kinda looks like a sandy dirt on a walling you will not have to worry about that till tyour in peaches casle and you find bowseer in a loked safe.
B )for tthae guy fighting the pink guy the first time around you will be obliterated but if your talking about the second time you just need some cunning if your talking about the third and final time when he turns into an ice pig thing you need alot of luck but i almost 100% the game so ive beaten him and the final boss but i nede to find one more bean and a feew other things.
c) for the guy stuck at plack beach with mario and luigi if youve made it to the top of the place alredy on the mounton and hw askes you to hit him youl need all the puzzel puieces from dimble wood to get him to help you . but if you have figured that out and went to dimble wood go back to the place that the yello catapillar guys guarding and ask him to go through hell make you find all the pieces outside of the zone hes protecting and thats when youl go in MARIO WILL GET CAPTUTRED and youl have to use luigi to SAVE him.
i hope this awnserd most of your questions because my arms are tired
. sorry for grammer issues.