First thing that may be needed is a parrelel flow condensor, but it should only be done if the items below can't get it to your satisfaction. The condensor will cool the liquid much better than the round type condensor that our trucks use. But, this should be a last resort as it will require the system to be evacuated again, and will most likely require different hoses to accomodate the new fittings.
Plug the holes with black silicone, it is more than enough to handle the temps of the refrigerant flowing in and out.
How much refrigerant did you put into the system? A general rule of thumb is to use about 80% of the R12 that would have been in the system. So if it called for 1 lb of R12, you would use about .8 lbs of R134. Too much can cause very high pressures, and a poor cooling effect.
You should also replace the orifice with a R134 one for better flow control. Do this only if you have to clear the system, as it will require disassembly of the lines.
Since you mentioned that the holes for the evaporator were open, you will probably want to clean the evaporator with brake clean to get better airflow through it. Openings like those can allow grease and other debris into the evaporator which will reduce the airflow, and can cause less cooling of the air. Do not use carb cleaner, as it will leave a residue and the odor is nearly impossible to get to clear out. Brake cleaner leaves no residue and the odor can usually be cleared by running the blower for a few minutes.
In general on the systems I have done, they may not be as cold, but you don't really notice much of a difference. The better the fan works at pulling air through the condensor, the cooler the air inside will be.
