Implied in every landlord-tenant arrangement is what's called the "Covenant of Quiet Enjoyment", which basically means that as a tenant, you have the right to quiet use and enjoyment of the premises without interference from the landlord. This is your home, and no one is allowed to enter your home without your permission - let him know as much.
Hopefully, this can be handled in a nice civil conversation, but if not, then be sure to let him know that if he continues to come in uninvited, that you may pursue whatever legal recourse necessary to keep your home free from intrusion.
Regarding repairs, you as a tenant have a duty to keep the premises in reasonably good repair, (like keeping the yard clean of dog poo)
But, when a condition exists that threatens your basic living requirements, you should tell your landlord about it. If the landlord does nothing about it, typically, your recourse is to (1) move, (2) repair the condition yourself and deduct the amount used to repair from the rent, (3) reduce the rent or withhold it until the landlord responds to the condition, or (4) remain and seek an action to recover damages.
If the landlord does respond to repair a condition, which may have happened here, such a response does not give the landlord free reign to come and go as he pleases. You both should mutually agree upon date and time of entry for repairs.
Regarding rent collection, talk to your landlord and set up a set time on each first of the month when you're able to meet him and give him the rent. If the time he shows up is unreasonable, then let him know. Just because he is a landlord doesn't mean that common courtesy gets thrown out the window! I'm sure if you politely tell him that you'd like to get dressed and have your morning coffee before handing him the check, I would think that he'd understand.
Do you notice a theme here? Communication with your landlord is key. If talking doesn't work, send a letter (even certify it if you feel the need to do so) and create a paper trail. If things continue to deteriorate, then consult an attorney.
Finally, READ YOUR LEASE! There may be other remedies other than what I've mention, and as always, consult an attorney in your jurisdiction - there may be some local rules that apply.