Knee Discomfort and blisters are they connected?

Hi all

i am a relative newbie - i started running begining of the year 5 stone over weight and have gradually increased my running and following a healthy eating plan and completed my first 5K event last sunday.  I am still however 3 and a half stone overweight but im continuing my training for a 10k event in september.

Thing is ive always suffered with knee aches after running- i have always put it down to my size.  It generally lasts for up to two days after running sometimes noticable enough to need ibuprofen to take edge off but it generally goes enough in time for my next run- i run every other day.

 Also when i first started running i went to a running shop in february i had my gait looked at and they gave me running shoes appropiate.  However lately i have been getting some killer blisters on the inside of my right foot by the top of the arch.   And during that time my knee aches are more noticable too.

Im just wondering if all this is interlinked?  Can my gait change from when i first started running?  do i simply need a thicker pair of socks?

not sure if visiting running shop again would help the aches and pains... or whether this is to be expected given my current size and will improve as i loose more weight and improve general fitness.

thoughts and tips on this issue greatly appreciated!  thanks in advance