Thanks for your comments guys, I'll try out your ideas, looks like it was too hot from your comments, there was this brown liquid buildup.I was trying out some custom settings at the same time. Temp at 215-210 °c rather than the usual lower 205-200. Or might have to change the hotend completely. The print bed is much knackered now. I was rushing to put a print job. Lessons learnt.

Wasn't expecting the hotend to get clogged towards the end after @4hr printing

I carry out the following steps before each print- On the printer itself-(1) auto-home (2) then switch on auto-levelling (3) then auto-level. This steps have been working great for me. I dont bother with the pronterface anymore.

I came to the same conclusion but for aligning the y-axis. Undid the top 2 screws and the bottom four that secure the z- axis to the base and stepper. Then i aligned the y-axis with the lines on the print-bed. Only then, i tightened the top two nut-bolts and the bottom four screws. My x and y axis are now completely aligned with the print bed markings during travel.

Caterpillar print with limited joint

Tried some changes myself as follows: