I would like to know if the Court order has more importance than the
Practice Direction and as a litigant in person, can prepare the bundle
A court order issued in a particular lawsuit has priority over a general rule of procedure.
It is not clear from the context provided if the Court direction that the Applicant's solicitor" do something, when you do not have a solicitor, means that the Court was using sloppy wording and intended that you do it, or reflects the fact that the Court forgot that you didn't have a solicitor and would have required the other party to do it if it had remembered that fact. Both possibilities are plausible in this situation.
The Court's Order is even more ambiguous in light of the fact that the next sentence in 3.1 which you omit from the quoted material in the question, states that:
Where all the parties are litigants in person none of them shall,
unless the court otherwise directs, be obliged to provide a bundle,
but any bundle which they choose to lodge must be prepared and lodged
so as to comply with this practice direction.
When in doubt concerning that kind of ambiguity the best course of action would be to contact the office of the judge in charge of the case and ask the clerk or assistant who answers what you should do, or what the judge's order means. That person will give you an answer, or have the court consider the matter and issue a new clarified order, or direct you to someone else with whom you can discuss your question.
It also isn't entirely impossible that the order given to you was actually intended for another case entirely and that the judge or someone in the judge's office simply got confused and entered the order in the wrong case. I've experienced that kind of inadvertent mistake by a judge (getting a court order meant for someone else in a different case in one of my cases) once every couple of years as a practicing attorney. It's rare, but it does happen.