First of all, try to relax as much as you can when you give him meds - he can sense if you are afraid.
You can try wrapping him in a towel to help you hold him securely while medicating him.
Have everything ready ahead of time before you pick him up. The quicker you are, the less time he has to get fidgety.
If you carefully push the syringe in at one side of his mouth until he starts grinding on it, you can then adminster the medication knowing he is swallowing.
Some medications taste good, so piggies will usually take them easily. Others don't taste so good I guess and they might fight them.
Some of those meds you mentioned are for motility, to keep his gut moving (cisapride and metaclopramide). The baytril is the antibiotic to cure his respiratory illness. Metronidazole is an anti parasitic medication and Diphenhydramine is an antihistamine (Benadryl).
I know how it feels to have a piggie on so many meds. It can seem endless. Are you hand feeding?? You have to keep lots of food moving through his system. I hope you have posted on guinealynx because they will be able to give you awesome advice there to help you through. I know from experience when you've had a slowdown in motility, you have to be aggressive with the handfeeding and that they can take two steps forward, one step back sometimes.
You should also be giving him probiotics since he is on the baytril. You can use something like acidphilus capsules (sprinkle the powder on his food or dissolve it and syringe it to him) or you can use something like benebac. You can even use fresh poop from a healthy piggie (poop soup). It will help restore the proper balance in his gut.
Good luck with him and please keep us updated!